From a31040e055e38f8a530a99fcc865b2bf9f2e14b9 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Mon, 18 Mar 2024 15:16:00 +0100
Subject: [PATCH 01/58] Generate reports per lane, group and rundir

---
 conf/modules.config       |  20 ++++++-
 main.nf                   |   5 +-
 workflows/seqinspector.nf | 120 ++++++++++++++++++++++++++++++++++----
 3 files changed, 133 insertions(+), 12 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index e3ea8fa..296ca78 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -35,7 +35,25 @@ process {
         publishDir = [
             path: { "${params.outdir}/multiqc" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            saveAs: {
+                filename -> 
+                    switch (filename) {
+                        case 'versions.yml':
+                            null
+                            break
+                        case ~/L\d+_multiqc_(report\.html|plots|data)/:
+                            "lanes/L${(filename =~ /L(\d+)_multiqc_(report\.html|plots|data)/)[0][1]}/${filename}"
+                            break
+                        case ~/G-.+_multiqc_(report\.html|plots|data)/:
+                            "groups/G-${(filename =~ /G-(.+)_multiqc_(report\.html|plots|data)/)[0][1]}/${filename}"
+                            break
+                        case ~/D-.+_multiqc_(report\.html|plots|data)/:
+                            "rundirs/D-${(filename =~ /D-(.+)_multiqc_(report\.html|plots|data)/)[0][1]}/${filename}"
+                            break
+                        default:
+                            filename
+                    }
+            }
         ]
     }
 
diff --git a/main.nf b/main.nf
index 1e9c2ed..58afd1f 100644
--- a/main.nf
+++ b/main.nf
@@ -58,7 +58,10 @@ workflow NFCORE_SEQINSPECTOR {
     )
 
     emit:
-    multiqc_report = SEQINSPECTOR.out.multiqc_report // channel: /path/to/multiqc_report.html
+    global_report = SEQINSPECTOR.out.global_report // channel: /path/to/multiqc_report.html
+    lane_reports = SEQINSPECTOR.out.lane_reports // channel: /path/to/multiqc_report.html
+    group_report = SEQINSPECTOR.out.group_reports // channel: /path/to/multiqc_report.html
+    rundir_report = SEQINSPECTOR.out.rundir_reports // channel: /path/to/multiqc_report.html
 
 }
 /*
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 9ae3384..b6fd3bc 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -5,7 +5,10 @@
 */
 
 include { FASTQC                 } from '../modules/nf-core/fastqc/main'
-include { MULTIQC                } from '../modules/nf-core/multiqc/main'
+include { MULTIQC } from '../modules/nf-core/multiqc/main'
+include { MULTIQC as MULTIQC_PER_LANE } from '../modules/nf-core/multiqc/main'
+include { MULTIQC as MULTIQC_PER_GROUP } from '../modules/nf-core/multiqc/main'
+include { MULTIQC as MULTIQC_PER_RUNDIR } from '../modules/nf-core/multiqc/main'
 include { paramsSummaryMap       } from 'plugin/nf-validation'
 include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
@@ -26,6 +29,8 @@ workflow SEQINSPECTOR {
 
     ch_versions = Channel.empty()
     ch_multiqc_files = Channel.empty()
+    ch_multiqc_extra_files = Channel.empty()
+    ch_multiqc_reports = Channel.empty()
 
     //
     // MODULE: Run FastQC
@@ -33,7 +38,7 @@ workflow SEQINSPECTOR {
     FASTQC (
         ch_samplesheet
     )
-    ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]})
+    ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip)
     ch_versions = ch_versions.mix(FASTQC.out.versions.first())
 
     //
@@ -46,26 +51,121 @@ workflow SEQINSPECTOR {
     //
     // MODULE: MultiQC
     //
-    ch_multiqc_config                     = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
-    ch_multiqc_custom_config              = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty()
+    ch_multiqc_config              = params.multiqc_config ? 
+        Channel.fromPath(params.multiqc_config, checkIfExists: true) :
+        Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
     ch_multiqc_logo                       = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty()
     summary_params                        = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
     ch_workflow_summary                   = Channel.value(paramsSummaryMultiqc(summary_params))
     ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
     ch_methods_description                = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description))
-    ch_multiqc_files                      = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
-    ch_multiqc_files                      = ch_multiqc_files.mix(ch_collated_versions)
-    ch_multiqc_files                      = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: false))
+    ch_multiqc_extra_files                      = ch_multiqc_extra_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
+    ch_multiqc_extra_files                      = ch_multiqc_extra_files.mix(ch_collated_versions)
+    ch_multiqc_extra_files                      = ch_multiqc_extra_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: false))
 
     MULTIQC (
-        ch_multiqc_files.collect(),
+        ch_multiqc_files
+            .map { meta, file -> file }
+            .mix(ch_multiqc_extra_files)
+            .collect(),
         ch_multiqc_config.toList(),
-        ch_multiqc_custom_config.toList(),
+        Channel.empty().toList(),
+        ch_multiqc_logo.toList()
+    )
+
+    multiqc_extra_files = ch_multiqc_extra_files.toList()
+
+    // Generate reports by lane
+    lane_mqc_files = ch_multiqc_files
+        .map { meta, sample -> [ "L${meta.lane}", meta, sample ] }
+        .groupTuple()
+        .tap { mqc_by_lane }
+        .collectFile{
+            lane, meta, samples -> [
+                "${lane}_multiqc_extra_config.yml",
+                "output_fn_name: \"${lane}_multiqc_report.html\"\ndata_dir_name: \"${lane}_multiqc_data\"\nplots_dir_name: \"${lane}_multiqc_plots\""
+            ]
+        }
+        .map { file -> def fileparts = file.name.split("_")
+             [ fileparts[0], file ] 
+        }
+        .join(mqc_by_lane)
+        .multiMap { lane, config, meta , samples_per_lane ->
+            samples_per_lane: samples_per_lane
+            config: config
+        }
+
+    MULTIQC_PER_LANE(
+        lane_mqc_files.samples_per_lane
+            .map { samples -> samples + multiqc_extra_files.value },
+        ch_multiqc_config.toList(),
+        lane_mqc_files.config,
+        ch_multiqc_logo.toList()
+    )
+
+    // Generate reports by group
+    group_mqc_files = ch_multiqc_files
+        .filter { meta, sample -> meta.group }
+        .map { meta, sample -> [ "G-${meta.group}", meta, sample ] }
+        .groupTuple()
+        .tap { mqc_by_group }
+        .collectFile{
+            group, meta, samples -> [
+                "${group}_multiqc_extra_config.yml",
+                "output_fn_name: \"${group}_multiqc_report.html\"\ndata_dir_name: \"${group}_multiqc_data\"\nplots_dir_name: \"${group}_multiqc_plots\""
+            ]
+        }
+        .map { file -> def fileparts = file.name.split("_")
+             [ fileparts[0], file ] 
+        }
+        .join(mqc_by_group)
+        .multiMap { group, config, meta , samples_per_group ->
+            samples_per_group: samples_per_group
+            config: config
+        }
+
+    MULTIQC_PER_GROUP(
+        group_mqc_files.samples_per_group
+            .map { samples -> samples + multiqc_extra_files.value },
+        ch_multiqc_config.toList(),
+        group_mqc_files.config,
+        ch_multiqc_logo.toList()
+    )
+
+    // Generate reports by rundir
+    rundir_mqc_files = ch_multiqc_files
+        .filter { meta, sample -> meta.rundir }
+        .map { meta, sample -> [ "D-${meta.rundir.name}", meta, sample ] }
+        .groupTuple()
+        .tap { mqc_by_rundir }
+        .collectFile{
+            rundir, meta, samples -> [
+                "${rundir}_multiqc_extra_config.yml",
+                "output_fn_name: \"${rundir}_multiqc_report.html\"\ndata_dir_name: \"${rundir}_multiqc_data\"\nplots_dir_name: \"${rundir}_multiqc_plots\""
+            ]
+        }
+        .map { file -> def fileparts = file.name.split("_")
+             [ fileparts[0], file ] 
+        }
+        .join(mqc_by_rundir)
+        .multiMap { rundir, config, meta , samples_per_rundir ->
+            samples_per_rundir: samples_per_rundir
+            config: config
+        }
+
+    MULTIQC_PER_RUNDIR(
+        rundir_mqc_files.samples_per_rundir
+            .map { samples -> samples + multiqc_extra_files.value },
+        ch_multiqc_config.toList(),
+        rundir_mqc_files.config,
         ch_multiqc_logo.toList()
     )
 
     emit:
-    multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html
+    global_report = MULTIQC.out.report.toList()             // channel: /path/to/multiqc_report.html
+    lane_reports = MULTIQC_PER_LANE.out.report.toList() // channel: [ /path/to/multiqc_report.html ]
+    group_reports = MULTIQC_PER_GROUP.out.report.toList() // channel: [ /path/to/multiqc_report.html ]
+    rundir_reports = MULTIQC_PER_RUNDIR.out.report.toList() // channel: [ /path/to/multiqc_report.html ]
     versions       = ch_versions                 // channel: [ path(versions.yml) ]
 }
 

From 0da58701e706f23001df33bf997bf671ea37a787 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Thu, 28 Mar 2024 16:21:45 +0100
Subject: [PATCH 02/58] Improve formatting

---
 conf/modules.config       |  2 +-
 main.nf                   |  6 ++--
 workflows/seqinspector.nf | 71 +++++++++++++++++++++++++--------------
 3 files changed, 50 insertions(+), 29 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 296ca78..8b7a9c6 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -52,7 +52,7 @@ process {
                             break
                         default:
                             filename
-                    }
+                }
             }
         ]
     }
diff --git a/main.nf b/main.nf
index 58afd1f..1ee043e 100644
--- a/main.nf
+++ b/main.nf
@@ -58,9 +58,9 @@ workflow NFCORE_SEQINSPECTOR {
     )
 
     emit:
-    global_report = SEQINSPECTOR.out.global_report // channel: /path/to/multiqc_report.html
-    lane_reports = SEQINSPECTOR.out.lane_reports // channel: /path/to/multiqc_report.html
-    group_report = SEQINSPECTOR.out.group_reports // channel: /path/to/multiqc_report.html
+    global_report = SEQINSPECTOR.out.global_report  // channel: /path/to/multiqc_report.html
+    lane_reports = SEQINSPECTOR.out.lane_reports    // channel: /path/to/multiqc_report.html
+    group_report = SEQINSPECTOR.out.group_reports   // channel: /path/to/multiqc_report.html
     rundir_report = SEQINSPECTOR.out.rundir_reports // channel: /path/to/multiqc_report.html
 
 }
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index b6fd3bc..f0a269a 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -4,15 +4,17 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { FASTQC                 } from '../modules/nf-core/fastqc/main'
-include { MULTIQC } from '../modules/nf-core/multiqc/main'
-include { MULTIQC as MULTIQC_PER_LANE } from '../modules/nf-core/multiqc/main'
-include { MULTIQC as MULTIQC_PER_GROUP } from '../modules/nf-core/multiqc/main'
+include { FASTQC                        } from '../modules/nf-core/fastqc/main'
+
+include { MULTIQC                       } from '../modules/nf-core/multiqc/main'
+include { MULTIQC as MULTIQC_PER_LANE   } from '../modules/nf-core/multiqc/main'
+include { MULTIQC as MULTIQC_PER_GROUP  } from '../modules/nf-core/multiqc/main'
 include { MULTIQC as MULTIQC_PER_RUNDIR } from '../modules/nf-core/multiqc/main'
-include { paramsSummaryMap       } from 'plugin/nf-validation'
-include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pipeline'
-include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
-include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_seqinspector_pipeline'
+
+include { paramsSummaryMap              } from 'plugin/nf-validation'
+include { paramsSummaryMultiqc          } from '../subworkflows/nf-core/utils_nfcore_pipeline'
+include { softwareVersionsToYAML        } from '../subworkflows/nf-core/utils_nfcore_pipeline'
+include { methodsDescriptionText        } from '../subworkflows/local/utils_nfcore_seqinspector_pipeline'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -27,10 +29,10 @@ workflow SEQINSPECTOR {
 
     main:
 
-    ch_versions = Channel.empty()
-    ch_multiqc_files = Channel.empty()
+    ch_versions            = Channel.empty()
+    ch_multiqc_files       = Channel.empty()
     ch_multiqc_extra_files = Channel.empty()
-    ch_multiqc_reports = Channel.empty()
+    ch_multiqc_reports     = Channel.empty()
 
     //
     // MODULE: Run FastQC
@@ -45,23 +47,42 @@ workflow SEQINSPECTOR {
     // Collate and save software versions
     //
     softwareVersionsToYAML(ch_versions)
-        .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_pipeline_software_mqc_versions.yml', sort: true, newLine: true)
-        .set { ch_collated_versions }
+        .collectFile(
+            storeDir: "${params.outdir}/pipeline_info",
+            name: 'nf_core_pipeline_software_mqc_versions.yml',
+            sort: true,
+            newLine: true
+        ).set { ch_collated_versions }
 
     //
     // MODULE: MultiQC
     //
-    ch_multiqc_config              = params.multiqc_config ? 
+    ch_multiqc_config = params.multiqc_config ?
         Channel.fromPath(params.multiqc_config, checkIfExists: true) :
         Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
-    ch_multiqc_logo                       = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty()
-    summary_params                        = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
-    ch_workflow_summary                   = Channel.value(paramsSummaryMultiqc(summary_params))
-    ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
-    ch_methods_description                = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description))
-    ch_multiqc_extra_files                      = ch_multiqc_extra_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
-    ch_multiqc_extra_files                      = ch_multiqc_extra_files.mix(ch_collated_versions)
-    ch_multiqc_extra_files                      = ch_multiqc_extra_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: false))
+    ch_multiqc_logo   = params.multiqc_logo ?
+        Channel.fromPath(params.multiqc_logo, checkIfExists: true) :
+        Channel.empty()
+
+    summary_params                        = paramsSummaryMap(
+        workflow, parameters_schema: "nextflow_schema.json")
+    ch_workflow_summary                   = Channel.value(
+        paramsSummaryMultiqc(summary_params))
+    ch_multiqc_custom_methods_description = params.multiqc_methods_description ?
+        file(params.multiqc_methods_description, checkIfExists: true) :
+        file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
+    ch_methods_description                = Channel.value(
+        methodsDescriptionText(ch_multiqc_custom_methods_description))
+
+    ch_multiqc_extra_files = ch_multiqc_extra_files.mix(
+        ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
+    ch_multiqc_extra_files = ch_multiqc_extra_files.mix(ch_collated_versions)
+    ch_multiqc_extra_files = ch_multiqc_extra_files.mix(
+        ch_methods_description.collectFile(
+            name: 'methods_description_mqc.yaml',
+            sort: false
+        )
+    )
 
     MULTIQC (
         ch_multiqc_files
@@ -163,10 +184,10 @@ workflow SEQINSPECTOR {
 
     emit:
     global_report = MULTIQC.out.report.toList()             // channel: /path/to/multiqc_report.html
-    lane_reports = MULTIQC_PER_LANE.out.report.toList() // channel: [ /path/to/multiqc_report.html ]
-    group_reports = MULTIQC_PER_GROUP.out.report.toList() // channel: [ /path/to/multiqc_report.html ]
+    lane_reports = MULTIQC_PER_LANE.out.report.toList()     // channel: [ /path/to/multiqc_report.html ]
+    group_reports = MULTIQC_PER_GROUP.out.report.toList()   // channel: [ /path/to/multiqc_report.html ]
     rundir_reports = MULTIQC_PER_RUNDIR.out.report.toList() // channel: [ /path/to/multiqc_report.html ]
-    versions       = ch_versions                 // channel: [ path(versions.yml) ]
+    versions       = ch_versions                            // channel: [ path(versions.yml) ]
 }
 
 /*

From d233d8f4052208b4e572ddb1e8d561387df1cce5 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Thu, 28 Mar 2024 16:56:51 +0100
Subject: [PATCH 03/58] Improve output sorting

---
 conf/modules.config | 18 +++++++++++++++---
 1 file changed, 15 insertions(+), 3 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 8b7a9c6..3b2fc02 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -42,13 +42,25 @@ process {
                             null
                             break
                         case ~/L\d+_multiqc_(report\.html|plots|data)/:
-                            "lanes/L${(filename =~ /L(\d+)_multiqc_(report\.html|plots|data)/)[0][1]}/${filename}"
+                            def lane = (filename =~ /L(\d+)_multiqc_(report\.html|plots|data)/)[0][1]
+                            def new_filename = filename.replaceFirst(
+                                "(?<prefix>.*)L${lane}_(?<suffix>multiqc_(report\\.html|plots|data).*)",
+                                '${prefix}${suffix}')
+                            "lanes/L${lane}/${new_filename}"
                             break
                         case ~/G-.+_multiqc_(report\.html|plots|data)/:
-                            "groups/G-${(filename =~ /G-(.+)_multiqc_(report\.html|plots|data)/)[0][1]}/${filename}"
+                            def group = (filename =~ /G-(.+)_multiqc_(report\.html|plots|data)/)[0][1]
+                            def new_filename = filename.replaceFirst(
+                                "(?<prefix>.*)G-${group}_(?<suffix>multiqc_(report\\.html|plots|data).*)",
+                                '${prefix}${suffix}')
+                            "groups/${group}/${new_filename}"
                             break
                         case ~/D-.+_multiqc_(report\.html|plots|data)/:
-                            "rundirs/D-${(filename =~ /D-(.+)_multiqc_(report\.html|plots|data)/)[0][1]}/${filename}"
+                            def rundir = (filename =~ /D-(.+)_multiqc_(report\.html|plots|data)/)[0][1]
+                            def new_filename = filename.replaceFirst(
+                                "(?<prefix>.*)D-${rundir}_(?<suffix>multiqc_(report\\.html|plots|data).*)",
+                                '${prefix}${suffix}')
+                            "rundirs/${rundir}/${new_filename}"
                             break
                         default:
                             filename

From 307e43c6a21c77ad30c8f02997c3220568d35fb2 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Mon, 8 Apr 2024 14:11:47 +0200
Subject: [PATCH 04/58] Use `group` instead of `project`

---
 assets/schema_input.json                                      | 4 ++--
 subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/assets/schema_input.json b/assets/schema_input.json
index 9fb321b..1648944 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -19,11 +19,11 @@
                 "errorMessage": "Lane ID must be a number",
                 "meta": ["lane"]
             },
-            "project": {
+            "group": {
                 "type": "string",
                 "pattern": "^\\S+$",
                 "errorMessage": "Project ID cannot contain spaces",
-                "meta": ["project"]
+                "meta": ["group"]
             },
             "fastq_1": {
                 "type": "string",
diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index cdbb640..e1f8e4d 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -84,7 +84,7 @@ workflow PIPELINE_INITIALISATION {
         .fromSamplesheet("input") // Validates samplesheet against $projectDir/assets/schema_input.json. Path to validation schema is defined by $projectDir/nextflow_schema.json
         .map {
             meta, fastq_1, fastq_2 ->
-                def id_string = "${meta.sample}_${meta.project ?: "ungrouped"}_${meta.lane}"
+                def id_string = "${meta.sample}_${meta.group ?: "ungrouped"}_${meta.lane}"
                 def updated_meta = meta + [ id: id_string ]
                 if (!fastq_2) {
                     return [ updated_meta.id, updated_meta + [ single_end:true ], [ fastq_1 ] ]

From 627cf940a2a6b5f7cca7cbb692af1cf74293a289 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Mon, 8 Apr 2024 14:21:59 +0200
Subject: [PATCH 05/58] Fix output channel

---
 main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/main.nf b/main.nf
index 1ee043e..9de4f94 100644
--- a/main.nf
+++ b/main.nf
@@ -104,7 +104,7 @@ workflow {
         params.outdir,
         params.monochrome_logs,
         params.hook_url,
-        NFCORE_SEQINSPECTOR.out.multiqc_report
+        NFCORE_SEQINSPECTOR.out.global_report,
     )
 }
 

From c9ba02866dc35a1b345476645ece7f9a6e48cc8b Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Mon, 8 Apr 2024 14:22:17 +0200
Subject: [PATCH 06/58] Fix linting

---
 conf/modules.config                                         | 2 +-
 .../local/utils_nfcore_seqinspector_pipeline/main.nf        | 1 -
 workflows/seqinspector.nf                                   | 6 +++---
 3 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 3b2fc02..44a3513 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -36,7 +36,7 @@ process {
             path: { "${params.outdir}/multiqc" },
             mode: params.publish_dir_mode,
             saveAs: {
-                filename -> 
+                filename ->
                     switch (filename) {
                         case 'versions.yml':
                             null
diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index e1f8e4d..9001400 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -101,7 +101,6 @@ workflow PIPELINE_INITIALISATION {
         //     meta, fastqs ->
         //         return [ meta, fastqs.flatten() ]
         // }
-        .view()
         .set { ch_samplesheet }
 
     emit:
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index f0a269a..815bc40 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -108,7 +108,7 @@ workflow SEQINSPECTOR {
             ]
         }
         .map { file -> def fileparts = file.name.split("_")
-             [ fileparts[0], file ] 
+            [ fileparts[0], file ]
         }
         .join(mqc_by_lane)
         .multiMap { lane, config, meta , samples_per_lane ->
@@ -137,7 +137,7 @@ workflow SEQINSPECTOR {
             ]
         }
         .map { file -> def fileparts = file.name.split("_")
-             [ fileparts[0], file ] 
+            [ fileparts[0], file ]
         }
         .join(mqc_by_group)
         .multiMap { group, config, meta , samples_per_group ->
@@ -166,7 +166,7 @@ workflow SEQINSPECTOR {
             ]
         }
         .map { file -> def fileparts = file.name.split("_")
-             [ fileparts[0], file ] 
+            [ fileparts[0], file ]
         }
         .join(mqc_by_rundir)
         .multiMap { rundir, config, meta , samples_per_rundir ->

From 2cfc91d449bac7c1a6d22d125fd57e3d8592a51b Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Mon, 8 Apr 2024 15:48:41 +0200
Subject: [PATCH 07/58] Give credits back to NGI

---
 README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 5e2bc4c..abe0d4e 100644
--- a/README.md
+++ b/README.md
@@ -80,11 +80,11 @@ For more details about the output files and reports, please refer to the
 
 ## Credits
 
-nf-core/seqinspector was originally written by Adrien Coulier.
+nf-core/seqinspector was originally written by the Swedish [@NationalGenomicsInfrastructure](https://github.com/NationalGenomicsInfrastructure/).
 
 We thank the following people for their extensive assistance in the development of this pipeline:
 
-<!-- TODO nf-core: If applicable, make list of people who have also contributed -->
+- [@mahesh-panchal](https://github.com/mahesh-panchal)
 
 ## Contributions and Support
 

From fbfb02dbba5945fcfcf8d431cccd7a230eea5ff5 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Tue, 9 Apr 2024 09:26:32 +0200
Subject: [PATCH 08/58] Fix file names

---
 conf/modules.config       | 18 +++++++++---------
 workflows/seqinspector.nf | 24 ++++++++++++++++++------
 2 files changed, 27 insertions(+), 15 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 44a3513..b2e48f3 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -41,24 +41,24 @@ process {
                         case 'versions.yml':
                             null
                             break
-                        case ~/L\d+_multiqc_(report\.html|plots|data)/:
-                            def lane = (filename =~ /L(\d+)_multiqc_(report\.html|plots|data)/)[0][1]
+                        case ~/\[LANE:\d+\]_multiqc_(report\.html|plots|data)/:
+                            def lane = (filename =~ /\[LANE:(\d+)\]_multiqc_(report\.html|plots|data)/)[0][1]
                             def new_filename = filename.replaceFirst(
-                                "(?<prefix>.*)L${lane}_(?<suffix>multiqc_(report\\.html|plots|data).*)",
+                                "(?<prefix>.*)\\[LANE:${lane}\\]_(?<suffix>multiqc_(report\\.html|plots|data).*)",
                                 '${prefix}${suffix}')
                             "lanes/L${lane}/${new_filename}"
                             break
-                        case ~/G-.+_multiqc_(report\.html|plots|data)/:
-                            def group = (filename =~ /G-(.+)_multiqc_(report\.html|plots|data)/)[0][1]
+                        case ~/\[GROUP:.+\]_multiqc_(report\.html|plots|data)/:
+                            def group = (filename =~ /\[GROUP:(.+)\]_multiqc_(report\.html|plots|data)/)[0][1]
                             def new_filename = filename.replaceFirst(
-                                "(?<prefix>.*)G-${group}_(?<suffix>multiqc_(report\\.html|plots|data).*)",
+                                "(?<prefix>.*)\\[GROUP:${group}\\]_(?<suffix>multiqc_(report\\.html|plots|data).*)",
                                 '${prefix}${suffix}')
                             "groups/${group}/${new_filename}"
                             break
-                        case ~/D-.+_multiqc_(report\.html|plots|data)/:
-                            def rundir = (filename =~ /D-(.+)_multiqc_(report\.html|plots|data)/)[0][1]
+                        case ~/\[RUNDIR:.+\]_multiqc_(report\.html|plots|data)/:
+                            def rundir = (filename =~ /\[RUNDIR:(.+)\]_multiqc_(report\.html|plots|data)/)[0][1]
                             def new_filename = filename.replaceFirst(
-                                "(?<prefix>.*)D-${rundir}_(?<suffix>multiqc_(report\\.html|plots|data).*)",
+                                "(?<prefix>.*)\\[RUNDIR:${rundir}\\]_(?<suffix>multiqc_(report\\.html|plots|data).*)",
                                 '${prefix}${suffix}')
                             "rundirs/${rundir}/${new_filename}"
                             break
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 815bc40..2acafc3 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -98,13 +98,17 @@ workflow SEQINSPECTOR {
 
     // Generate reports by lane
     lane_mqc_files = ch_multiqc_files
-        .map { meta, sample -> [ "L${meta.lane}", meta, sample ] }
+        .map { meta, sample -> [ "[LANE:${meta.lane}]", meta, sample ] }
         .groupTuple()
         .tap { mqc_by_lane }
         .collectFile{
             lane, meta, samples -> [
                 "${lane}_multiqc_extra_config.yml",
-                "output_fn_name: \"${lane}_multiqc_report.html\"\ndata_dir_name: \"${lane}_multiqc_data\"\nplots_dir_name: \"${lane}_multiqc_plots\""
+                """
+                    |output_fn_name: \"${lane}_multiqc_report.html\"
+                    |data_dir_name:  \"${lane}_multiqc_data\"
+                    |plots_dir_name: \"${lane}_multiqc_plots\"
+                """.stripMargin()
             ]
         }
         .map { file -> def fileparts = file.name.split("_")
@@ -127,13 +131,17 @@ workflow SEQINSPECTOR {
     // Generate reports by group
     group_mqc_files = ch_multiqc_files
         .filter { meta, sample -> meta.group }
-        .map { meta, sample -> [ "G-${meta.group}", meta, sample ] }
+        .map { meta, sample -> [ "[GROUP:${meta.group}]", meta, sample ] }
         .groupTuple()
         .tap { mqc_by_group }
         .collectFile{
             group, meta, samples -> [
                 "${group}_multiqc_extra_config.yml",
-                "output_fn_name: \"${group}_multiqc_report.html\"\ndata_dir_name: \"${group}_multiqc_data\"\nplots_dir_name: \"${group}_multiqc_plots\""
+                """
+                    |output_fn_name: \"${group}_multiqc_report.html\"
+                    |data_dir_name:  \"${group}_multiqc_data\"
+                    |plots_dir_name: \"${group}_multiqc_plots\"
+                """.stripMargin()
             ]
         }
         .map { file -> def fileparts = file.name.split("_")
@@ -156,13 +164,17 @@ workflow SEQINSPECTOR {
     // Generate reports by rundir
     rundir_mqc_files = ch_multiqc_files
         .filter { meta, sample -> meta.rundir }
-        .map { meta, sample -> [ "D-${meta.rundir.name}", meta, sample ] }
+        .map { meta, sample -> [ "[RUNDIR:${meta.rundir.name}]", meta, sample ] }
         .groupTuple()
         .tap { mqc_by_rundir }
         .collectFile{
             rundir, meta, samples -> [
                 "${rundir}_multiqc_extra_config.yml",
-                "output_fn_name: \"${rundir}_multiqc_report.html\"\ndata_dir_name: \"${rundir}_multiqc_data\"\nplots_dir_name: \"${rundir}_multiqc_plots\""
+                """
+                    |output_fn_name: \"${rundir}_multiqc_report.html\"
+                    |data_dir_name:  \"${rundir}_multiqc_data\"
+                    |plots_dir_name: \"${rundir}_multiqc_plots\"
+                """.stripMargin()
             ]
         }
         .map { file -> def fileparts = file.name.split("_")

From 8a19929d03832ecaf95a50962898882de04e6884 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Fri, 3 May 2024 09:50:42 +0200
Subject: [PATCH 09/58] Set up tests

---
 .gitignore                           |  1 +
 nf-test.config                       |  8 ++++++++
 tests/main.nf.test                   | 20 +++++++++++++++++++
 tests/nextflow.config                |  5 +++++
 tests/workflows/seqinspector.nf.test | 30 ++++++++++++++++++++++++++++
 5 files changed, 64 insertions(+)
 create mode 100644 nf-test.config
 create mode 100644 tests/main.nf.test
 create mode 100644 tests/nextflow.config
 create mode 100644 tests/workflows/seqinspector.nf.test

diff --git a/.gitignore b/.gitignore
index 5124c9a..089a407 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,3 +6,4 @@ results/
 testing/
 testing*
 *.pyc
+.nf-test
diff --git a/nf-test.config b/nf-test.config
new file mode 100644
index 0000000..6969c08
--- /dev/null
+++ b/nf-test.config
@@ -0,0 +1,8 @@
+config {
+
+    testsDir "tests"
+    workDir ".nf-test"
+    configFile "tests/nextflow.config"
+    profile "test,docker"
+
+}
diff --git a/tests/main.nf.test b/tests/main.nf.test
new file mode 100644
index 0000000..72498b5
--- /dev/null
+++ b/tests/main.nf.test
@@ -0,0 +1,20 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf"
+    script "main.nf"
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                outdir = "tests/results"
+            }
+        }
+
+        then {
+            assert workflow.success
+        }
+
+    }
+
+}
diff --git a/tests/nextflow.config b/tests/nextflow.config
new file mode 100644
index 0000000..c19b1ad
--- /dev/null
+++ b/tests/nextflow.config
@@ -0,0 +1,5 @@
+/*
+========================================================================================
+    Nextflow config file for running tests
+========================================================================================
+*/
diff --git a/tests/workflows/seqinspector.nf.test b/tests/workflows/seqinspector.nf.test
new file mode 100644
index 0000000..bbb529d
--- /dev/null
+++ b/tests/workflows/seqinspector.nf.test
@@ -0,0 +1,30 @@
+nextflow_workflow {
+
+    name "Test Workflow SEQINSPECTOR"
+    script "workflows/seqinspector.nf"
+    workflow "SEQINSPECTOR"
+
+    test("Should run without failures pipeline") {
+
+        when {
+            params {
+                // define parameters here. Example:
+                // outdir = "tests/results"
+            }
+            workflow {
+                """
+                // define inputs of the workflow here. Example:
+                // input[0] = file("https://raw.githubusercontent.com/nf-core/test-datasets/e47966b63444ec0fcdef23bfc410eeca22535ac7/testdata/MiSeq/samplesheet.csv")
+                input[0] = file("assets/samplesheet.csv")
+                """
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert snapshot(workflow.out).match()
+        }
+
+    }
+
+}

From eba628ef9389a13214e6c9663965d6ea56d7e994 Mon Sep 17 00:00:00 2001
From: kedhammar <alfred.kedhammar@scilifelab.se>
Date: Fri, 3 May 2024 12:18:42 +0200
Subject: [PATCH 10/58] point test conf upstream

---
 conf/test.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/test.config b/conf/test.config
index 38e9ee3..2c26a9c 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -22,7 +22,7 @@ params {
     // Input data
     // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
-    input  = 'https://raw.githubusercontent.com/KarNair/test-datasets/seqinspector/testdata/MiSeq/samplesheet.csv'
+    input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/seqinspector/testdata/MiSeq/samplesheet.csv'
 
     // Genome references
     genome = 'R64-1-1'

From 23f69d1302457fc32295c3c77bd41d443bb96d9e Mon Sep 17 00:00:00 2001
From: kedhammar <alfred.kedhammar@scilifelab.se>
Date: Fri, 3 May 2024 13:05:47 +0200
Subject: [PATCH 11/58] project -> group

---
 assets/samplesheet.csv | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv
index fbe5de2..fef3b4e 100644
--- a/assets/samplesheet.csv
+++ b/assets/samplesheet.csv
@@ -1,3 +1,3 @@
-sample,lane,project,fastq_1,fastq_2,rundir
+sample,lane,group,fastq_1,fastq_2,rundir
 SAMPLE_PAIRED_END,1,P001,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz,/path/to/rundir
 SAMPLE_SINGLE_END,2,P002,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,/path/to/rundir

From 1ebf3f1adc86f3c50020a56f95430b06f3a5000a Mon Sep 17 00:00:00 2001
From: kedhammar <alfred.kedhammar@scilifelab.se>
Date: Fri, 3 May 2024 13:06:48 +0200
Subject: [PATCH 12/58] project -> group

---
 assets/schema_input.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/assets/schema_input.json b/assets/schema_input.json
index 1648944..7115bfa 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -22,7 +22,7 @@
             "group": {
                 "type": "string",
                 "pattern": "^\\S+$",
-                "errorMessage": "Project ID cannot contain spaces",
+                "errorMessage": "Group ID cannot contain spaces",
                 "meta": ["group"]
             },
             "fastq_1": {

From b0bf471667c0547654afd14d668e8f70aab55185 Mon Sep 17 00:00:00 2001
From: kedhammar <alfred.kedhammar@scilifelab.se>
Date: Fri, 3 May 2024 13:53:31 +0200
Subject: [PATCH 13/58] make lane non-compulsory

---
 assets/schema_input.json  | 2 +-
 workflows/seqinspector.nf | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/assets/schema_input.json b/assets/schema_input.json
index 7115bfa..c9800d5 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -47,7 +47,7 @@
                 "meta": ["rundir"]
             }
         },
-        "required": ["sample", "lane", "fastq_1"],
+        "required": ["sample", "fastq_1"],
         "dependentRequired": {
             "fastq_2": ["fastq_1"]
         }
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 2acafc3..018e079 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -98,6 +98,7 @@ workflow SEQINSPECTOR {
 
     // Generate reports by lane
     lane_mqc_files = ch_multiqc_files
+        .filter { meta, sample -> meta.lane }
         .map { meta, sample -> [ "[LANE:${meta.lane}]", meta, sample ] }
         .groupTuple()
         .tap { mqc_by_lane }

From 9e0eca39baf5b58760ec4117b4faefde4a512f09 Mon Sep 17 00:00:00 2001
From: kedhammar <alfred.kedhammar@scilifelab.se>
Date: Fri, 3 May 2024 15:59:10 +0200
Subject: [PATCH 14/58] remove unused file

---
 assets/samplesheet.csv | 3 ---
 1 file changed, 3 deletions(-)
 delete mode 100644 assets/samplesheet.csv

diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv
deleted file mode 100644
index fef3b4e..0000000
--- a/assets/samplesheet.csv
+++ /dev/null
@@ -1,3 +0,0 @@
-sample,lane,group,fastq_1,fastq_2,rundir
-SAMPLE_PAIRED_END,1,P001,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz,/path/to/rundir
-SAMPLE_SINGLE_END,2,P002,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,/path/to/rundir

From 98e60bf160cb6a4476d55b38a44095e67f79eeea Mon Sep 17 00:00:00 2001
From: kedhammar <alfred.kedhammar@scilifelab.se>
Date: Fri, 3 May 2024 16:38:52 +0200
Subject: [PATCH 15/58] revamp nf-test, run once for each sequencing platform

---
 tests/MiSeq.main.nf.test             | 23 +++++++++++++++++++++
 tests/NovaSeq6000.main.nf.test       | 23 +++++++++++++++++++++
 tests/PromethION.main.nf.test        | 23 +++++++++++++++++++++
 tests/main.nf.test                   | 20 -------------------
 tests/nextflow.config                | 11 ++++++++++
 tests/workflows/seqinspector.nf.test | 30 ----------------------------
 6 files changed, 80 insertions(+), 50 deletions(-)
 create mode 100644 tests/MiSeq.main.nf.test
 create mode 100644 tests/NovaSeq6000.main.nf.test
 create mode 100644 tests/PromethION.main.nf.test
 delete mode 100644 tests/main.nf.test
 delete mode 100644 tests/workflows/seqinspector.nf.test

diff --git a/tests/MiSeq.main.nf.test b/tests/MiSeq.main.nf.test
new file mode 100644
index 0000000..0246a75
--- /dev/null
+++ b/tests/MiSeq.main.nf.test
@@ -0,0 +1,23 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf on MiSeq data"
+    script "../main.nf"
+    tag "seqinspector"
+    tag "PIPELINE"
+
+    test("MiSeq data test") {
+
+        when {
+            params {
+                outdir = "tests/results/MiSeq"
+                input  = "https://raw.githubusercontent.com/nf-core/test-datasets/seqinspector/testdata/MiSeq/samplesheet.csv"
+            }
+        }
+
+        then {
+            assert workflow.success
+        }
+
+    }
+
+}
diff --git a/tests/NovaSeq6000.main.nf.test b/tests/NovaSeq6000.main.nf.test
new file mode 100644
index 0000000..7c410e5
--- /dev/null
+++ b/tests/NovaSeq6000.main.nf.test
@@ -0,0 +1,23 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf on NovaSeq6000 data"
+    script "../main.nf"
+    tag "seqinspector"
+    tag "PIPELINE"
+
+    test("NovaSeq6000 data test") {
+
+        when {
+            params {
+                outdir = "tests/results/NovaSeq6000"
+                input  = "https://raw.githubusercontent.com/nf-core/test-datasets/seqinspector/testdata/NovaSeq6000/samplesheet.csv"
+            }
+        }
+
+        then {
+            assert workflow.success
+        }
+
+    }
+
+}
diff --git a/tests/PromethION.main.nf.test b/tests/PromethION.main.nf.test
new file mode 100644
index 0000000..9987c95
--- /dev/null
+++ b/tests/PromethION.main.nf.test
@@ -0,0 +1,23 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf on PromethION data"
+    script "../main.nf"
+    tag "seqinspector"
+    tag "PIPELINE"
+
+    test("PromethION data test") {
+
+        when {
+            params {
+                outdir = "tests/results/PromethION"
+                input  = "https://raw.githubusercontent.com/nf-core/test-datasets/seqinspector/testdata/PromethION/samplesheet.csv"
+            }
+        }
+
+        then {
+            assert workflow.success
+        }
+
+    }
+
+}
diff --git a/tests/main.nf.test b/tests/main.nf.test
deleted file mode 100644
index 72498b5..0000000
--- a/tests/main.nf.test
+++ /dev/null
@@ -1,20 +0,0 @@
-nextflow_pipeline {
-
-    name "Test Workflow main.nf"
-    script "main.nf"
-
-    test("Should run without failures") {
-
-        when {
-            params {
-                outdir = "tests/results"
-            }
-        }
-
-        then {
-            assert workflow.success
-        }
-
-    }
-
-}
diff --git a/tests/nextflow.config b/tests/nextflow.config
index c19b1ad..422545b 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -3,3 +3,14 @@
     Nextflow config file for running tests
 ========================================================================================
 */
+
+params {
+    config_profile_name        = 'nf-test profile'
+    config_profile_description = 'Configuration profile to use for nf-test.'
+
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus   = 2
+    max_memory = '3.GB'
+    max_time   = '2.h'
+
+}
diff --git a/tests/workflows/seqinspector.nf.test b/tests/workflows/seqinspector.nf.test
deleted file mode 100644
index bbb529d..0000000
--- a/tests/workflows/seqinspector.nf.test
+++ /dev/null
@@ -1,30 +0,0 @@
-nextflow_workflow {
-
-    name "Test Workflow SEQINSPECTOR"
-    script "workflows/seqinspector.nf"
-    workflow "SEQINSPECTOR"
-
-    test("Should run without failures pipeline") {
-
-        when {
-            params {
-                // define parameters here. Example:
-                // outdir = "tests/results"
-            }
-            workflow {
-                """
-                // define inputs of the workflow here. Example:
-                // input[0] = file("https://raw.githubusercontent.com/nf-core/test-datasets/e47966b63444ec0fcdef23bfc410eeca22535ac7/testdata/MiSeq/samplesheet.csv")
-                input[0] = file("assets/samplesheet.csv")
-                """
-            }
-        }
-
-        then {
-            assert workflow.success
-            assert snapshot(workflow.out).match()
-        }
-
-    }
-
-}

From d95c660d8fbdba413920d45a7f7025e9261989c0 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Mon, 6 May 2024 15:54:05 +0200
Subject: [PATCH 16/58] Update modules and subworkflows

---
 modules.json                                       | 4 ++--
 modules/nf-core/fastqc/main.nf                     | 6 ++++++
 subworkflows/nf-core/utils_nfcore_pipeline/main.nf | 8 +++++++-
 3 files changed, 15 insertions(+), 3 deletions(-)

diff --git a/modules.json b/modules.json
index ebbc5dc..87fe816 100644
--- a/modules.json
+++ b/modules.json
@@ -7,7 +7,7 @@
                 "nf-core": {
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c",
+                        "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
@@ -26,7 +26,7 @@
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfvalidation_plugin": {
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index 9e19a74..d79f1c8 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -25,6 +25,11 @@ process FASTQC {
     def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] }
     def rename_to = old_new_pairs*.join(' ').join(' ')
     def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
+
+    def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB')
+    // FastQC memory value allowed range (100 - 10000)
+    def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb)
+
     """
     printf "%s %s\\n" $rename_to | while read old_name new_name; do
         [ -f "\${new_name}" ] || ln -s \$old_name \$new_name
@@ -33,6 +38,7 @@ process FASTQC {
     fastqc \\
         $args \\
         --threads $task.cpus \\
+        --memory $fastqc_memory \\
         $renamed_files
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index a8b55d6..14558c3 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -65,9 +65,15 @@ def checkProfileProvided(nextflow_cli_args) {
 // Citation string for pipeline
 //
 def workflowCitation() {
+    def temp_doi_ref = ""
+    String[] manifest_doi = workflow.manifest.doi.tokenize(",")
+    // Using a loop to handle multiple DOIs
+    // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
+    // Removing ` ` since the manifest.doi is a string and not a proper list
+    for (String doi_ref: manifest_doi) temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
     return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
         "* The pipeline\n" +
-        "  ${workflow.manifest.doi}\n\n" +
+        temp_doi_ref + "\n" +
         "* The nf-core framework\n" +
         "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
         "* Software dependencies\n" +

From e0527ccb6c235fcb01f5fa26e1b192e705b3f873 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Tue, 7 May 2024 16:45:09 +0200
Subject: [PATCH 17/58] Fix multiqc extra files

Issue with the previous implementation was that sometimes
MULTIQC_PER_LANE would execute before the extra files were collected
into `ch_multiqc_extra_files`, causing `null` to be added to the list of
files passed to multiqc.
---
 workflows/seqinspector.nf | 35 +++++++++++++++++++++++++++--------
 1 file changed, 27 insertions(+), 8 deletions(-)

diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 018e079..65343a8 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -94,11 +94,17 @@ workflow SEQINSPECTOR {
         ch_multiqc_logo.toList()
     )
 
-    multiqc_extra_files = ch_multiqc_extra_files.toList()
-
     // Generate reports by lane
+    multiqc_extra_files_per_lane = ch_multiqc_files
+        .filter { meta, sample -> meta.lane }
+        .map { meta, sample -> meta.lane }
+        .unique()
+        .map { lane -> [lane:lane] }
+        .cross(ch_multiqc_extra_files)
+
     lane_mqc_files = ch_multiqc_files
         .filter { meta, sample -> meta.lane }
+        .mix(multiqc_extra_files_per_lane)
         .map { meta, sample -> [ "[LANE:${meta.lane}]", meta, sample ] }
         .groupTuple()
         .tap { mqc_by_lane }
@@ -122,16 +128,23 @@ workflow SEQINSPECTOR {
         }
 
     MULTIQC_PER_LANE(
-        lane_mqc_files.samples_per_lane
-            .map { samples -> samples + multiqc_extra_files.value },
+        lane_mqc_files.samples_per_lane,
         ch_multiqc_config.toList(),
         lane_mqc_files.config,
         ch_multiqc_logo.toList()
     )
 
     // Generate reports by group
+    multiqc_extra_files_per_group = ch_multiqc_files
+        .filter { meta, sample -> meta.group }
+        .map { meta, sample -> meta.group }
+        .unique()
+        .map { group -> [group:group] }
+        .cross(ch_multiqc_extra_files)
+
     group_mqc_files = ch_multiqc_files
         .filter { meta, sample -> meta.group }
+        .mix(multiqc_extra_files_per_group)
         .map { meta, sample -> [ "[GROUP:${meta.group}]", meta, sample ] }
         .groupTuple()
         .tap { mqc_by_group }
@@ -155,16 +168,23 @@ workflow SEQINSPECTOR {
         }
 
     MULTIQC_PER_GROUP(
-        group_mqc_files.samples_per_group
-            .map { samples -> samples + multiqc_extra_files.value },
+        group_mqc_files.samples_per_group,
         ch_multiqc_config.toList(),
         group_mqc_files.config,
         ch_multiqc_logo.toList()
     )
 
     // Generate reports by rundir
+    multiqc_extra_files_per_rundir = ch_multiqc_files
+        .filter { meta, sample -> meta.rundir }
+        .map { meta, sample -> meta.rundir }
+        .unique()
+        .map { rundir -> [rundir:rundir] }
+        .cross(ch_multiqc_extra_files)
+
     rundir_mqc_files = ch_multiqc_files
         .filter { meta, sample -> meta.rundir }
+        .mix(multiqc_extra_files_per_rundir)
         .map { meta, sample -> [ "[RUNDIR:${meta.rundir.name}]", meta, sample ] }
         .groupTuple()
         .tap { mqc_by_rundir }
@@ -188,8 +208,7 @@ workflow SEQINSPECTOR {
         }
 
     MULTIQC_PER_RUNDIR(
-        rundir_mqc_files.samples_per_rundir
-            .map { samples -> samples + multiqc_extra_files.value },
+        rundir_mqc_files.samples_per_rundir,
         ch_multiqc_config.toList(),
         rundir_mqc_files.config,
         ch_multiqc_logo.toList()

From 93c66a40091d6228c28a965af19f0aa64dfe9f0d Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Wed, 8 May 2024 14:01:12 +0000
Subject: [PATCH 18/58] Template update for nf-core/tools version 2.14.0

---
 .editorconfig                                 |   6 +-
 .github/PULL_REQUEST_TEMPLATE.md              |   2 +-
 .github/workflows/awsfulltest.yml             |  10 +-
 .github/workflows/awstest.yml                 |  12 +-
 .github/workflows/ci.yml                      |   4 +-
 .github/workflows/download_pipeline.yml       |  22 ++-
 .github/workflows/fix-linting.yml             |   6 +-
 .github/workflows/linting.yml                 |  18 +-
 .github/workflows/linting_comment.yml         |   2 +-
 .github/workflows/release-announcements.yml   |   6 +-
 .nf-core.yml                                  |   1 +
 .pre-commit-config.yaml                       |   3 +
 README.md                                     |   2 +-
 conf/base.config                              |   3 -
 conf/modules.config                           |   8 -
 conf/test.config                              |   2 +-
 conf/test_full.config                         |   2 +-
 docs/usage.md                                 |   2 +
 modules.json                                  |   4 +-
 modules/nf-core/fastqc/main.nf                |   6 +
 nextflow.config                               | 176 +++++++++---------
 nextflow_schema.json                          |   7 +
 pyproject.toml                                |  15 --
 .../main.nf                                   |  16 +-
 .../nf-core/utils_nfcore_pipeline/main.nf     |   8 +-
 workflows/seqinspector.nf                     |  46 +++--
 26 files changed, 220 insertions(+), 169 deletions(-)
 delete mode 100644 pyproject.toml

diff --git a/.editorconfig b/.editorconfig
index dd9ffa5..72dda28 100644
--- a/.editorconfig
+++ b/.editorconfig
@@ -28,10 +28,6 @@ indent_style = unset
 [/assets/email*]
 indent_size = unset
 
-# ignore Readme
-[README.md]
-indent_style = unset
-
-# ignore python
+# ignore python and markdown
 [*.{py,md}]
 indent_style = unset
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index 5d27c53..6de151f 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/seqi
 - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/seqinspector/tree/master/.github/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/seqinspector _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core lint`).
-- [ ] Ensure the test suite passes (`nf-test test main.nf.test -profile test,docker`).
+- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index 1b153a6..9278410 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -8,12 +8,12 @@ on:
     types: [published]
   workflow_dispatch:
 jobs:
-  run-tower:
+  run-platform:
     name: Run AWS full tests
     if: github.repository == 'nf-core/seqinspector'
     runs-on: ubuntu-latest
     steps:
-      - name: Launch workflow via tower
+      - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
         # TODO nf-core: You can customise AWS full pipeline tests as required
         # Add full size test data (but still relatively small datasets for few samples)
@@ -33,7 +33,7 @@ jobs:
 
       - uses: actions/upload-artifact@v4
         with:
-          name: Tower debug log file
+          name: Seqera Platform debug log file
           path: |
-            tower_action_*.log
-            tower_action_*.json
+            seqera_platform_action_*.log
+            seqera_platform_action_*.json
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
index 6def58c..eef6f2c 100644
--- a/.github/workflows/awstest.yml
+++ b/.github/workflows/awstest.yml
@@ -5,13 +5,13 @@ name: nf-core AWS test
 on:
   workflow_dispatch:
 jobs:
-  run-tower:
+  run-platform:
     name: Run AWS tests
     if: github.repository == 'nf-core/seqinspector'
     runs-on: ubuntu-latest
     steps:
-      # Launch workflow using Tower CLI tool action
-      - name: Launch workflow via tower
+      # Launch workflow using Seqera Platform CLI tool action
+      - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
@@ -27,7 +27,7 @@ jobs:
 
       - uses: actions/upload-artifact@v4
         with:
-          name: Tower debug log file
+          name: Seqera Platform debug log file
           path: |
-            tower_action_*.log
-            tower_action_*.json
+            seqera_platform_action_*.log
+            seqera_platform_action_*.json
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 7a2be9a..59c9410 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -28,10 +28,10 @@ jobs:
           - "latest-everything"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
         with:
           version: "${{ matrix.NXF_VER }}"
 
diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index 08622fd..2d20d64 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -14,6 +14,8 @@ on:
   pull_request:
     types:
       - opened
+      - edited
+      - synchronize
     branches:
       - master
   pull_request_target:
@@ -28,11 +30,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - name: Disk space cleanup
+        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           architecture: "x64"
       - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7
         with:
@@ -65,8 +70,17 @@ jobs:
       - name: Inspect download
         run: tree ./${{ env.REPOTITLE_LOWERCASE }}
 
-      - name: Run the downloaded pipeline
+      - name: Run the downloaded pipeline (stub)
+        id: stub_run_pipeline
+        continue-on-error: true
         env:
           NXF_SINGULARITY_CACHEDIR: ./
           NXF_SINGULARITY_HOME_MOUNT: true
         run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
+      - name: Run the downloaded pipeline (stub run not supported)
+        id: run_pipeline
+        if: ${{ job.steps.stub_run_pipeline.status == failure() }}
+        env:
+          NXF_SINGULARITY_CACHEDIR: ./
+          NXF_SINGULARITY_HOME_MOUNT: true
+        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
index 45e0686..1984e17 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix-linting.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -32,9 +32,9 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       # Install and run pre-commit
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: 3.11
+          python-version: "3.12"
 
       - name: Install pre-commit
         run: pip install pre-commit
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 073e187..a3fb254 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -14,12 +14,12 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
-      - name: Set up Python 3.11
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - name: Set up Python 3.12
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: 3.11
+          python-version: "3.12"
           cache: "pip"
 
       - name: Install pre-commit
@@ -32,14 +32,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           architecture: "x64"
 
       - name: Install dependencies
@@ -60,7 +60,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
+        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
         with:
           name: linting-logs
           path: |
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index b706875..40acc23 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3
+        uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3
         with:
           workflow: linting.yml
           workflow_conclusion: completed
diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
index d468aea..03ecfcf 100644
--- a/.github/workflows/release-announcements.yml
+++ b/.github/workflows/release-announcements.yml
@@ -12,7 +12,7 @@ jobs:
       - name: get topics and convert to hashtags
         id: get_topics
         run: |
-          curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' >> $GITHUB_OUTPUT
+          echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')"  >> $GITHUB_OUTPUT
 
       - uses: rzr/fediverse-action@master
         with:
@@ -25,13 +25,13 @@ jobs:
 
             Please see the changelog: ${{ github.event.release.html_url }}
 
-            ${{ steps.get_topics.outputs.GITHUB_OUTPUT }} #nfcore #openscience #nextflow #bioinformatics
+            ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics
 
   send-tweet:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: "3.10"
       - name: Install dependencies
diff --git a/.nf-core.yml b/.nf-core.yml
index 3805dc8..d6daa40 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1 +1,2 @@
 repository_type: pipeline
+nf_core_version: "2.14.0"
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index af57081..4dc0f1d 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -3,6 +3,9 @@ repos:
     rev: "v3.1.0"
     hooks:
       - id: prettier
+        additional_dependencies:
+          - prettier@3.2.5
+
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
     rev: "2.7.3"
     hooks:
diff --git a/README.md b/README.md
index 5e2bc4c..bfb53fe 100644
--- a/README.md
+++ b/README.md
@@ -13,7 +13,7 @@
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
-[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/seqinspector)
+[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)
 
 [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
 
diff --git a/conf/base.config b/conf/base.config
index 8d7dffc..aab50f9 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -59,7 +59,4 @@ process {
         errorStrategy = 'retry'
         maxRetries    = 2
     }
-    withName:CUSTOM_DUMPSOFTWAREVERSIONS {
-        cache = false
-    }
 }
diff --git a/conf/modules.config b/conf/modules.config
index e3ea8fa..d203d2b 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -22,14 +22,6 @@ process {
         ext.args = '--quiet'
     }
 
-    withName: CUSTOM_DUMPSOFTWAREVERSIONS {
-        publishDir = [
-            path: { "${params.outdir}/pipeline_info" },
-            mode: params.publish_dir_mode,
-            pattern: '*_versions.yml'
-        ]
-    }
-
     withName: 'MULTIQC' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [
diff --git a/conf/test.config b/conf/test.config
index fbbffdd..6a7b984 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -22,7 +22,7 @@ params {
     // Input data
     // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
-    input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'
+    input  = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'
 
     // Genome references
     genome = 'R64-1-1'
diff --git a/conf/test_full.config b/conf/test_full.config
index 6fbea31..53b2288 100644
--- a/conf/test_full.config
+++ b/conf/test_full.config
@@ -17,7 +17,7 @@ params {
     // Input data for full size test
     // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv'
+    input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv'
 
     // Genome references
     genome = 'R64-1-1'
diff --git a/docs/usage.md b/docs/usage.md
index f926de7..ec180e4 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -156,6 +156,8 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
   - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/)
 - `apptainer`
   - A generic configuration profile to be used with [Apptainer](https://apptainer.org/)
+- `wave`
+  - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow ` 24.03.0-edge` or later).
 - `conda`
   - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer.
 
diff --git a/modules.json b/modules.json
index ebbc5dc..87fe816 100644
--- a/modules.json
+++ b/modules.json
@@ -7,7 +7,7 @@
                 "nf-core": {
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c",
+                        "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
@@ -26,7 +26,7 @@
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfvalidation_plugin": {
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index 9e19a74..d79f1c8 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -25,6 +25,11 @@ process FASTQC {
     def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] }
     def rename_to = old_new_pairs*.join(' ').join(' ')
     def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
+
+    def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB')
+    // FastQC memory value allowed range (100 - 10000)
+    def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb)
+
     """
     printf "%s %s\\n" $rename_to | while read old_name new_name; do
         [ -f "\${new_name}" ] || ln -s \$old_name \$new_name
@@ -33,6 +38,7 @@ process FASTQC {
     fastqc \\
         $args \\
         --threads $task.cpus \\
+        --memory $fastqc_memory \\
         $renamed_files
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/nextflow.config b/nextflow.config
index 776814f..a73f66b 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -16,7 +16,8 @@ params {
     genome                     = null
     igenomes_base              = 's3://ngi-igenomes/igenomes/'
     igenomes_ignore            = false
-    fasta                      = null// MultiQC options
+
+    // MultiQC options
     multiqc_config             = null
     multiqc_title              = null
     multiqc_logo               = null
@@ -24,15 +25,16 @@ params {
     multiqc_methods_description = null
 
     // Boilerplate options
-    outdir                     = null
-    publish_dir_mode           = 'copy'
-    email                      = null
-    email_on_fail              = null
-    plaintext_email            = false
-    monochrome_logs            = false
-    hook_url                   = null
-    help                       = false
-    version                    = false
+    outdir                       = null
+    publish_dir_mode             = 'copy'
+    email                        = null
+    email_on_fail                = null
+    plaintext_email              = false
+    monochrome_logs              = false
+    hook_url                     = null
+    help                         = false
+    version                      = false
+    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
 
     // Config options
     config_profile_name        = null
@@ -68,103 +70,109 @@ try {
 }
 
 // Load nf-core/seqinspector custom profiles from different institutions.
-// Warning: Uncomment only if a pipeline-specific institutional config already exists on nf-core/configs!
-// try {
-//   includeConfig "${params.custom_config_base}/pipeline/seqinspector.config"
-// } catch (Exception e) {
-//   System.err.println("WARNING: Could not load nf-core/config/seqinspector profiles: ${params.custom_config_base}/pipeline/seqinspector.config")
-// }
+try {
+    includeConfig "${params.custom_config_base}/pipeline/seqinspector.config"
+} catch (Exception e) {
+    System.err.println("WARNING: Could not load nf-core/config/seqinspector profiles: ${params.custom_config_base}/pipeline/seqinspector.config")
+}
 profiles {
     debug {
-        dumpHashes             = true
-        process.beforeScript   = 'echo $HOSTNAME'
-        cleanup                = false
+        dumpHashes              = true
+        process.beforeScript    = 'echo $HOSTNAME'
+        cleanup                 = false
         nextflow.enable.configProcessNamesValidation = true
     }
     conda {
-        conda.enabled          = true
-        docker.enabled         = false
-        singularity.enabled    = false
-        podman.enabled         = false
-        shifter.enabled        = false
-        charliecloud.enabled   = false
-        channels               = ['conda-forge', 'bioconda', 'defaults']
-        apptainer.enabled      = false
+        conda.enabled           = true
+        docker.enabled          = false
+        singularity.enabled     = false
+        podman.enabled          = false
+        shifter.enabled         = false
+        charliecloud.enabled    = false
+        conda.channels          = ['conda-forge', 'bioconda', 'defaults']
+        apptainer.enabled       = false
     }
     mamba {
-        conda.enabled          = true
-        conda.useMamba         = true
-        docker.enabled         = false
-        singularity.enabled    = false
-        podman.enabled         = false
-        shifter.enabled        = false
-        charliecloud.enabled   = false
-        apptainer.enabled      = false
+        conda.enabled           = true
+        conda.useMamba          = true
+        docker.enabled          = false
+        singularity.enabled     = false
+        podman.enabled          = false
+        shifter.enabled         = false
+        charliecloud.enabled    = false
+        apptainer.enabled       = false
     }
     docker {
-        docker.enabled         = true
-        conda.enabled          = false
-        singularity.enabled    = false
-        podman.enabled         = false
-        shifter.enabled        = false
-        charliecloud.enabled   = false
-        apptainer.enabled      = false
-        docker.runOptions      = '-u $(id -u):$(id -g)'
+        docker.enabled          = true
+        conda.enabled           = false
+        singularity.enabled     = false
+        podman.enabled          = false
+        shifter.enabled         = false
+        charliecloud.enabled    = false
+        apptainer.enabled       = false
+        docker.runOptions       = '-u $(id -u):$(id -g)'
     }
     arm {
-        docker.runOptions      = '-u $(id -u):$(id -g) --platform=linux/amd64'
+        docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'
     }
     singularity {
-        singularity.enabled    = true
-        singularity.autoMounts = true
-        conda.enabled          = false
-        docker.enabled         = false
-        podman.enabled         = false
-        shifter.enabled        = false
-        charliecloud.enabled   = false
-        apptainer.enabled      = false
+        singularity.enabled     = true
+        singularity.autoMounts  = true
+        conda.enabled           = false
+        docker.enabled          = false
+        podman.enabled          = false
+        shifter.enabled         = false
+        charliecloud.enabled    = false
+        apptainer.enabled       = false
     }
     podman {
-        podman.enabled         = true
-        conda.enabled          = false
-        docker.enabled         = false
-        singularity.enabled    = false
-        shifter.enabled        = false
-        charliecloud.enabled   = false
-        apptainer.enabled      = false
+        podman.enabled          = true
+        conda.enabled           = false
+        docker.enabled          = false
+        singularity.enabled     = false
+        shifter.enabled         = false
+        charliecloud.enabled    = false
+        apptainer.enabled       = false
     }
     shifter {
-        shifter.enabled        = true
-        conda.enabled          = false
-        docker.enabled         = false
-        singularity.enabled    = false
-        podman.enabled         = false
-        charliecloud.enabled   = false
-        apptainer.enabled      = false
+        shifter.enabled         = true
+        conda.enabled           = false
+        docker.enabled          = false
+        singularity.enabled     = false
+        podman.enabled          = false
+        charliecloud.enabled    = false
+        apptainer.enabled       = false
     }
     charliecloud {
-        charliecloud.enabled   = true
-        conda.enabled          = false
-        docker.enabled         = false
-        singularity.enabled    = false
-        podman.enabled         = false
-        shifter.enabled        = false
-        apptainer.enabled      = false
+        charliecloud.enabled    = true
+        conda.enabled           = false
+        docker.enabled          = false
+        singularity.enabled     = false
+        podman.enabled          = false
+        shifter.enabled         = false
+        apptainer.enabled       = false
     }
     apptainer {
-        apptainer.enabled      = true
-        apptainer.autoMounts   = true
-        conda.enabled          = false
-        docker.enabled         = false
-        singularity.enabled    = false
-        podman.enabled         = false
-        shifter.enabled        = false
-        charliecloud.enabled   = false
+        apptainer.enabled       = true
+        apptainer.autoMounts    = true
+        conda.enabled           = false
+        docker.enabled          = false
+        singularity.enabled     = false
+        podman.enabled          = false
+        shifter.enabled         = false
+        charliecloud.enabled    = false
+    }
+    wave {
+        apptainer.ociAutoPull   = true
+        singularity.ociAutoPull = true
+        wave.enabled            = true
+        wave.freeze             = true
+        wave.strategy           = 'conda,container'
     }
     gitpod {
-        executor.name          = 'local'
-        executor.cpus          = 4
-        executor.memory        = 8.GB
+        executor.name           = 'local'
+        executor.cpus           = 4
+        executor.memory         = 8.GB
     }
     test      { includeConfig 'conf/test.config'      }
     test_full { includeConfig 'conf/test_full.config' }
diff --git a/nextflow_schema.json b/nextflow_schema.json
index ec323b9..36308a0 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -265,6 +265,13 @@
                     "description": "Validation of parameters in lenient more.",
                     "hidden": true,
                     "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)."
+                },
+                "pipelines_testdata_base_path": {
+                    "type": "string",
+                    "fa_icon": "far fa-check-circle",
+                    "description": "Base URL or local path to location of pipeline test dataset files",
+                    "default": "https://raw.githubusercontent.com/nf-core/test-datasets/",
+                    "hidden": true
                 }
             }
         }
diff --git a/pyproject.toml b/pyproject.toml
deleted file mode 100644
index 5611062..0000000
--- a/pyproject.toml
+++ /dev/null
@@ -1,15 +0,0 @@
-# Config file for Python. Mostly used to configure linting of bin/*.py with Ruff.
-# Should be kept the same as nf-core/tools to avoid fighting with template synchronisation.
-[tool.ruff]
-line-length = 120
-target-version = "py38"
-cache-dir = "~/.cache/ruff"
-
-[tool.ruff.lint]
-select = ["I", "E1", "E4", "E7", "E9", "F", "UP", "N"]
-
-[tool.ruff.lint.isort]
-known-first-party = ["nf_core"]
-
-[tool.ruff.lint.per-file-ignores]
-"__init__.py" = ["E402", "F401"]
diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index 56b144f..8728141 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -140,6 +140,10 @@ workflow PIPELINE_COMPLETION {
             imNotification(summary_params, hook_url)
         }
     }
+
+    workflow.onError {
+        log.error "Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting"
+    }
 }
 
 /*
@@ -230,8 +234,16 @@ def methodsDescriptionText(mqc_methods_yaml) {
     meta["manifest_map"] = workflow.manifest.toMap()
 
     // Pipeline DOI
-    meta["doi_text"] = meta.manifest_map.doi ? "(doi: <a href=\'https://doi.org/${meta.manifest_map.doi}\'>${meta.manifest_map.doi}</a>)" : ""
-    meta["nodoi_text"] = meta.manifest_map.doi ? "": "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"
+    if (meta.manifest_map.doi) {
+        // Using a loop to handle multiple DOIs
+        // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
+        // Removing ` ` since the manifest.doi is a string and not a proper list
+        def temp_doi_ref = ""
+        String[] manifest_doi = meta.manifest_map.doi.tokenize(",")
+        for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: <a href=\'https://doi.org/${doi_ref.replace("https://doi.org/", "").replace(" ", "")}\'>${doi_ref.replace("https://doi.org/", "").replace(" ", "")}</a>), "
+        meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length() - 2)
+    } else meta["doi_text"] = ""
+    meta["nodoi_text"] = meta.manifest_map.doi ? "" : "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"
 
     // Tool references
     meta["tool_citations"] = ""
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index a8b55d6..14558c3 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -65,9 +65,15 @@ def checkProfileProvided(nextflow_cli_args) {
 // Citation string for pipeline
 //
 def workflowCitation() {
+    def temp_doi_ref = ""
+    String[] manifest_doi = workflow.manifest.doi.tokenize(",")
+    // Using a loop to handle multiple DOIs
+    // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
+    // Removing ` ` since the manifest.doi is a string and not a proper list
+    for (String doi_ref: manifest_doi) temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
     return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
         "* The pipeline\n" +
-        "  ${workflow.manifest.doi}\n\n" +
+        temp_doi_ref + "\n" +
         "* The nf-core framework\n" +
         "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
         "* Software dependencies\n" +
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 9ae3384..cf7a85c 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -40,22 +40,44 @@ workflow SEQINSPECTOR {
     // Collate and save software versions
     //
     softwareVersionsToYAML(ch_versions)
-        .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_pipeline_software_mqc_versions.yml', sort: true, newLine: true)
-        .set { ch_collated_versions }
+        .collectFile(
+            storeDir: "${params.outdir}/pipeline_info",
+            name: 'nf_core_pipeline_software_mqc_versions.yml',
+            sort: true,
+            newLine: true
+        ).set { ch_collated_versions }
 
     //
     // MODULE: MultiQC
     //
-    ch_multiqc_config                     = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
-    ch_multiqc_custom_config              = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty()
-    ch_multiqc_logo                       = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty()
-    summary_params                        = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
-    ch_workflow_summary                   = Channel.value(paramsSummaryMultiqc(summary_params))
-    ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
-    ch_methods_description                = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description))
-    ch_multiqc_files                      = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
-    ch_multiqc_files                      = ch_multiqc_files.mix(ch_collated_versions)
-    ch_multiqc_files                      = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: false))
+    ch_multiqc_config        = Channel.fromPath(
+        "$projectDir/assets/multiqc_config.yml", checkIfExists: true)
+    ch_multiqc_custom_config = params.multiqc_config ?
+        Channel.fromPath(params.multiqc_config, checkIfExists: true) :
+        Channel.empty()
+    ch_multiqc_logo          = params.multiqc_logo ?
+        Channel.fromPath(params.multiqc_logo, checkIfExists: true) :
+        Channel.empty()
+
+    summary_params      = paramsSummaryMap(
+        workflow, parameters_schema: "nextflow_schema.json")
+    ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
+
+    ch_multiqc_custom_methods_description = params.multiqc_methods_description ?
+        file(params.multiqc_methods_description, checkIfExists: true) :
+        file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
+    ch_methods_description                = Channel.value(
+        methodsDescriptionText(ch_multiqc_custom_methods_description))
+
+    ch_multiqc_files = ch_multiqc_files.mix(
+        ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
+    ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)
+    ch_multiqc_files = ch_multiqc_files.mix(
+        ch_methods_description.collectFile(
+            name: 'methods_description_mqc.yaml',
+            sort: true
+        )
+    )
 
     MULTIQC (
         ch_multiqc_files.collect(),

From 88ca813165306088552d29cbf9ae4e93ae46a912 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Thu, 9 May 2024 11:43:27 +0000
Subject: [PATCH 19/58] Template update for nf-core/tools version 2.14.1

---
 .github/workflows/linting.yml | 1 -
 .nf-core.yml                  | 2 +-
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index a3fb254..1fcafe8 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -20,7 +20,6 @@ jobs:
         uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: "3.12"
-          cache: "pip"
 
       - name: Install pre-commit
         run: pip install pre-commit
diff --git a/.nf-core.yml b/.nf-core.yml
index d6daa40..e0b85a7 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,2 +1,2 @@
 repository_type: pipeline
-nf_core_version: "2.14.0"
+nf_core_version: "2.14.1"

From 42159a132e7f73f2594fcb0e66ca26702311cefb Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Tue, 14 May 2024 10:29:17 +0200
Subject: [PATCH 20/58] Add test snapshots

---
 tests/MiSeq.main.nf.test            | 25 +++++++++++++++---
 tests/MiSeq.main.nf.test.snap       | 19 ++++++++++++++
 tests/NovaSeq6000.main.nf.test      | 40 ++++++++++++++++++++++++++---
 tests/NovaSeq6000.main.nf.test.snap | 31 ++++++++++++++++++++++
 tests/PromethION.main.nf.test       | 20 ++++++++++++---
 tests/PromethION.main.nf.test.snap  | 15 +++++++++++
 workflows/seqinspector.nf           | 18 +++++--------
 7 files changed, 144 insertions(+), 24 deletions(-)
 create mode 100644 tests/MiSeq.main.nf.test.snap
 create mode 100644 tests/NovaSeq6000.main.nf.test.snap
 create mode 100644 tests/PromethION.main.nf.test.snap

diff --git a/tests/MiSeq.main.nf.test b/tests/MiSeq.main.nf.test
index 0246a75..1e72de9 100644
--- a/tests/MiSeq.main.nf.test
+++ b/tests/MiSeq.main.nf.test
@@ -9,15 +9,32 @@ nextflow_pipeline {
 
         when {
             params {
-                outdir = "tests/results/MiSeq"
+                outdir = "$outputDir"
                 input  = "https://raw.githubusercontent.com/nf-core/test-datasets/seqinspector/testdata/MiSeq/samplesheet.csv"
             }
         }
 
         then {
-            assert workflow.success
-        }
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    path("$outputDir/multiqc/lanes/L1/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/lanes/L1/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/lanes/L1/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/lanes/L1/multiqc_data/multiqc_software_versions.txt"),
 
-    }
+                    path("$outputDir/multiqc/groups/P001/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/groups/P001/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/groups/P001/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/groups/P001/multiqc_data/multiqc_software_versions.txt"),
 
+                    path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/multiqc_data/multiqc_software_versions.txt"),
+                    ).match()
+                }
+            )
+        }
+    }
 }
diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
new file mode 100644
index 0000000..e222b51
--- /dev/null
+++ b/tests/MiSeq.main.nf.test.snap
@@ -0,0 +1,19 @@
+{
+    "MiSeq data test": {
+        "content": [
+            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_fastqc.txt:md5,692b8aed0614ed1655f2c1cbea1ba312",
+            "multiqc_general_stats.txt:md5,630167d67d3f92408cd1a04422c7196f",
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
+            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_fastqc.txt:md5,692b8aed0614ed1655f2c1cbea1ba312",
+            "multiqc_general_stats.txt:md5,630167d67d3f92408cd1a04422c7196f",
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
+            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_fastqc.txt:md5,692b8aed0614ed1655f2c1cbea1ba312",
+            "multiqc_general_stats.txt:md5,630167d67d3f92408cd1a04422c7196f",
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95"
+        ],
+        "timestamp": "2024-05-08T16:29:33.284003"
+    }
+}
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test b/tests/NovaSeq6000.main.nf.test
index 7c410e5..f5de9aa 100644
--- a/tests/NovaSeq6000.main.nf.test
+++ b/tests/NovaSeq6000.main.nf.test
@@ -9,15 +9,47 @@ nextflow_pipeline {
 
         when {
             params {
-                outdir = "tests/results/NovaSeq6000"
+                outdir = "$outputDir"
                 input  = "https://raw.githubusercontent.com/nf-core/test-datasets/seqinspector/testdata/NovaSeq6000/samplesheet.csv"
             }
         }
 
         then {
-            assert workflow.success
-        }
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    path("$outputDir/multiqc/lanes/L1/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/lanes/L1/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/lanes/L1/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/lanes/L1/multiqc_data/multiqc_software_versions.txt"),
 
-    }
+                    path("$outputDir/multiqc/groups/S1/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/groups/S1/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/groups/S1/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/groups/S1/multiqc_data/multiqc_software_versions.txt"),
+
+                    path("$outputDir/multiqc/groups/S2/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/groups/S2/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/groups/S2/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/groups/S2/multiqc_data/multiqc_software_versions.txt"),
+
+                    path("$outputDir/multiqc/groups/S3/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/groups/S3/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/groups/S3/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/groups/S3/multiqc_data/multiqc_software_versions.txt"),
 
+                    path("$outputDir/multiqc/groups/S4/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/groups/S4/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/groups/S4/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/groups/S4/multiqc_data/multiqc_software_versions.txt"),
+
+                    path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/multiqc_data/multiqc_software_versions.txt"),
+                    ).match()
+                },
+            )
+        }
+    }
 }
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
new file mode 100644
index 0000000..a406b89
--- /dev/null
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -0,0 +1,31 @@
+{
+    "NovaSeq6000 data test": {
+        "content": [
+            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_fastqc.txt:md5,5ba3f4f4ec6026a5f5d55418384dcd3e",
+            "multiqc_general_stats.txt:md5,123cd6b64c9c15607405bcdd45a843d4",
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
+            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_fastqc.txt:md5,9b4fd8a6d6e8a9acabecd592f633472e",
+            "multiqc_general_stats.txt:md5,8237b88ceb018d3cb1edcea62d10f4a2",
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
+            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_fastqc.txt:md5,9246a5b6b7b0410c79049fc3dbd08e92",
+            "multiqc_general_stats.txt:md5,44328403f423c6f5ac9ee0a8a01e6725",
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
+            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_fastqc.txt:md5,84820276fae52d4d492831280ae6207c",
+            "multiqc_general_stats.txt:md5,dd07799e5e4b9d389f9de49a852c3363",
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
+            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_fastqc.txt:md5,59ae05d89453da6f57010ffb6466f902",
+            "multiqc_general_stats.txt:md5,e4629691992bfe639c01a84b90563334",
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
+            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_fastqc.txt:md5,5ba3f4f4ec6026a5f5d55418384dcd3e",
+            "multiqc_general_stats.txt:md5,123cd6b64c9c15607405bcdd45a843d4",
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95"
+        ],
+        "timestamp": "2024-05-14T10:17:35.440827"
+    }
+}
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test b/tests/PromethION.main.nf.test
index 9987c95..de2beb3 100644
--- a/tests/PromethION.main.nf.test
+++ b/tests/PromethION.main.nf.test
@@ -9,15 +9,27 @@ nextflow_pipeline {
 
         when {
             params {
-                outdir = "tests/results/PromethION"
+                outdir = "$outputDir"
                 input  = "https://raw.githubusercontent.com/nf-core/test-datasets/seqinspector/testdata/PromethION/samplesheet.csv"
             }
         }
 
         then {
-            assert workflow.success
-        }
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    path("$outputDir/multiqc/groups/r10p41_e8p2_human_runs_jkw/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/groups/r10p41_e8p2_human_runs_jkw/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/groups/r10p41_e8p2_human_runs_jkw/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/groups/r10p41_e8p2_human_runs_jkw/multiqc_data/multiqc_software_versions.txt"),
 
+                    path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/multiqc_data/multiqc_software_versions.txt"),
+                    ).match()
+                },
+            )
+        }
     }
-
 }
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
new file mode 100644
index 0000000..24e52bd
--- /dev/null
+++ b/tests/PromethION.main.nf.test.snap
@@ -0,0 +1,15 @@
+{
+    "PromethION data test": {
+        "content": [
+            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_fastqc.txt:md5,333360ff12007d64f2bf7673b0658bed",
+            "multiqc_general_stats.txt:md5,b1999255f9a502618d59be2f2e93bad2",
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
+            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+            "multiqc_fastqc.txt:md5,333360ff12007d64f2bf7673b0658bed",
+            "multiqc_general_stats.txt:md5,b1999255f9a502618d59be2f2e93bad2",
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95"
+        ],
+        "timestamp": "2024-05-08T17:17:23.151259"
+    }
+}
\ No newline at end of file
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 65343a8..3e2a08d 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -100,7 +100,7 @@ workflow SEQINSPECTOR {
         .map { meta, sample -> meta.lane }
         .unique()
         .map { lane -> [lane:lane] }
-        .cross(ch_multiqc_extra_files)
+        .combine(ch_multiqc_extra_files)
 
     lane_mqc_files = ch_multiqc_files
         .filter { meta, sample -> meta.lane }
@@ -118,9 +118,7 @@ workflow SEQINSPECTOR {
                 """.stripMargin()
             ]
         }
-        .map { file -> def fileparts = file.name.split("_")
-            [ fileparts[0], file ]
-        }
+        .map { file -> [ (file =~ /(\[LANE:.+\])/)[0][1], file ] }
         .join(mqc_by_lane)
         .multiMap { lane, config, meta , samples_per_lane ->
             samples_per_lane: samples_per_lane
@@ -140,7 +138,7 @@ workflow SEQINSPECTOR {
         .map { meta, sample -> meta.group }
         .unique()
         .map { group -> [group:group] }
-        .cross(ch_multiqc_extra_files)
+        .combine(ch_multiqc_extra_files)
 
     group_mqc_files = ch_multiqc_files
         .filter { meta, sample -> meta.group }
@@ -158,9 +156,7 @@ workflow SEQINSPECTOR {
                 """.stripMargin()
             ]
         }
-        .map { file -> def fileparts = file.name.split("_")
-            [ fileparts[0], file ]
-        }
+        .map { file -> [ (file =~ /(\[GROUP:.+\])/)[0][1], file ] }
         .join(mqc_by_group)
         .multiMap { group, config, meta , samples_per_group ->
             samples_per_group: samples_per_group
@@ -180,7 +176,7 @@ workflow SEQINSPECTOR {
         .map { meta, sample -> meta.rundir }
         .unique()
         .map { rundir -> [rundir:rundir] }
-        .cross(ch_multiqc_extra_files)
+        .combine(ch_multiqc_extra_files)
 
     rundir_mqc_files = ch_multiqc_files
         .filter { meta, sample -> meta.rundir }
@@ -198,9 +194,7 @@ workflow SEQINSPECTOR {
                 """.stripMargin()
             ]
         }
-        .map { file -> def fileparts = file.name.split("_")
-            [ fileparts[0], file ]
-        }
+        .map { file -> [ (file =~ /(\[RUNDIR:.+\])/)[0][1], file ] }
         .join(mqc_by_rundir)
         .multiMap { rundir, config, meta , samples_per_rundir ->
             samples_per_rundir: samples_per_rundir

From ef61f9f7e32f63235f0bf574a2fd89c1c119ffcf Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Tue, 14 May 2024 11:08:13 +0200
Subject: [PATCH 21/58] Remove unused module configuration

---
 conf/base.config    | 3 ---
 conf/modules.config | 8 --------
 2 files changed, 11 deletions(-)

diff --git a/conf/base.config b/conf/base.config
index 8d7dffc..aab50f9 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -59,7 +59,4 @@ process {
         errorStrategy = 'retry'
         maxRetries    = 2
     }
-    withName:CUSTOM_DUMPSOFTWAREVERSIONS {
-        cache = false
-    }
 }
diff --git a/conf/modules.config b/conf/modules.config
index b2e48f3..da3d2ca 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -22,14 +22,6 @@ process {
         ext.args = '--quiet'
     }
 
-    withName: CUSTOM_DUMPSOFTWAREVERSIONS {
-        publishDir = [
-            path: { "${params.outdir}/pipeline_info" },
-            mode: params.publish_dir_mode,
-            pattern: '*_versions.yml'
-        ]
-    }
-
     withName: 'MULTIQC' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [

From 51b01e98ca9560154634b08d541475abeffbc35c Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Tue, 14 May 2024 11:16:41 +0200
Subject: [PATCH 22/58] Update usage docs and restore example samplesheet

---
 assets/samplesheet.csv |  3 +++
 docs/usage.md          | 36 ++++++++++++------------------------
 2 files changed, 15 insertions(+), 24 deletions(-)
 create mode 100644 assets/samplesheet.csv

diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv
new file mode 100644
index 0000000..fef3b4e
--- /dev/null
+++ b/assets/samplesheet.csv
@@ -0,0 +1,3 @@
+sample,lane,group,fastq_1,fastq_2,rundir
+SAMPLE_PAIRED_END,1,P001,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz,/path/to/rundir
+SAMPLE_SINGLE_END,2,P002,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,/path/to/rundir
diff --git a/docs/usage.md b/docs/usage.md
index f926de7..df2be20 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -16,39 +16,27 @@ You will need to create a samplesheet with information about the samples you wou
 --input '[path to samplesheet file]'
 ```
 
-### Multiple runs of the same sample
-
-The `sample` identifiers have to be the same when you have re-sequenced the same sample more than once e.g. to increase sequencing depth. The pipeline will concatenate the raw reads before performing any downstream analysis. Below is an example for the same sample sequenced across 3 lanes:
-
-```csv title="samplesheet.csv"
-sample,fastq_1,fastq_2
-CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
-CONTROL_REP1,AEG588A1_S1_L003_R1_001.fastq.gz,AEG588A1_S1_L003_R2_001.fastq.gz
-CONTROL_REP1,AEG588A1_S1_L004_R1_001.fastq.gz,AEG588A1_S1_L004_R2_001.fastq.gz
-```
-
 ### Full samplesheet
 
-The pipeline will auto-detect whether a sample is single- or paired-end using the information provided in the samplesheet. The samplesheet can have as many columns as you desire, however, there is a strict requirement for the first 3 columns to match those defined in the table below.
-
-A final samplesheet file consisting of both single- and paired-end data may look something like the one below. This is for 6 samples, where `TREATMENT_REP3` has been sequenced twice.
-
 ```csv title="samplesheet.csv"
-sample,fastq_1,fastq_2
-CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
-CONTROL_REP2,AEG588A2_S2_L002_R1_001.fastq.gz,AEG588A2_S2_L002_R2_001.fastq.gz
-CONTROL_REP3,AEG588A3_S3_L002_R1_001.fastq.gz,AEG588A3_S3_L002_R2_001.fastq.gz
-TREATMENT_REP1,AEG588A4_S4_L003_R1_001.fastq.gz,
-TREATMENT_REP2,AEG588A5_S5_L003_R1_001.fastq.gz,
-TREATMENT_REP3,AEG588A6_S6_L003_R1_001.fastq.gz,
-TREATMENT_REP3,AEG588A6_S6_L004_R1_001.fastq.gz,
+sample,lane,group,fastq_1,fastq_2,rundir
+CONTROL_REP1,1,,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX
+CONTROL_REP2,1,,AEG588A2_S2_L002_R1_001.fastq.gz,AEG588A2_S2_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX
+CONTROL_REP3,1,,AEG588A3_S3_L002_R1_001.fastq.gz,AEG588A3_S3_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX
+TREATMENT_REP1,2,GROUP1,AEG588A4_S4_L003_R1_001.fastq.gz,,200624_A00834_0183_BHMTFYDRXX
+TREATMENT_REP2,2,GROUP1,AEG588A5_S5_L003_R1_001.fastq.gz,,200624_A00834_0183_BHMTFYDRXX
+TREATMENT_REP3,2,GROUP2,AEG588A6_S6_L003_R1_001.fastq.gz,,200624_A00834_0183_BHMTFYDRXX
+TREATMENT_REP3,2,GROUP2,AEG588A6_S6_L004_R1_001.fastq.gz,,200624_A00834_0183_BHMTFYDRXX
 ```
 
 | Column    | Description                                                                                                                                                                            |
 | --------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | `sample`  | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). |
+| `lane`    | Lane where the sample was processed on an Illumina instrument (optional).                                                                                                              |
+| `group`   | Group the sample belongs too, useful when several groups are pooled together (optional).                                                                                               |
+| `rundir`  | Path to the runfolder containing extra information about the sequencing run (optional) .                                                                                               |
 | `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".                                                             |
-| `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".                                                             |
+| `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz" (optional).                                                  |
 
 An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.
 

From 7c7f31f715a40c1f5b061099c9cd945214875ab0 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Tue, 14 May 2024 12:09:51 +0200
Subject: [PATCH 23/58] Update output docs

---
 docs/output.md | 27 +++++++++++++++++++++++++--
 1 file changed, 25 insertions(+), 2 deletions(-)

diff --git a/docs/output.md b/docs/output.md
index 77e4cc1..f83e1fa 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -6,8 +6,6 @@ This document describes the output produced by the pipeline. Most of the plots a
 
 The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory.
 
-<!-- TODO nf-core: Write this documentation describing your workflow's output -->
-
 ## Pipeline overview
 
 The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:
@@ -48,6 +46,31 @@ The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They m
   - `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser.
   - `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline.
   - `multiqc_plots/`: directory containing static images from the report in various formats.
+  - `lanes/` [1]
+    - `L1/`
+      - `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser.
+      - `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline.
+      - `multiqc_plots/`: directory containing static images from the report in various formats.
+    - `L2/`
+      - ...
+  - `groups/` [1]
+    - `GROUPNAME1/`
+      - `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser.
+      - `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline.
+      - `multiqc_plots/`: directory containing static images from the report in various formats.
+    - `GROUPNAME2/`
+      - ...
+  - `rundir/` [1]
+    - `RUNDIR1/`
+      - `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser.
+      - `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline.
+      - `multiqc_plots/`: directory containing static images from the report in various formats.
+    - `RUNDIR2/`
+      - ...
+
+
+[1] These files will only be generated if `lane`, `group` or `rundir` were specified for some samples.
+
 
 </details>
 

From 1c4f6e07019fad57bce6d5d3473155b2f3b364b3 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Tue, 14 May 2024 12:16:38 +0200
Subject: [PATCH 24/58] Update changelog

---
 CHANGELOG.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 58a53ef..6430add 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,8 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 
 ### `Added`
 
+- [#13](https://github.com/nf-core/seqinspector/pull/13) Generate reports per run, per project and per lane.
+
 ### `Fixed`
 
 ### `Dependencies`

From 211bfafb21f6f8c6b208d33875ddc9e45552973a Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Tue, 14 May 2024 12:20:34 +0200
Subject: [PATCH 25/58] Update samplesheet in readme file

---
 README.md | 11 ++---------
 1 file changed, 2 insertions(+), 9 deletions(-)

diff --git a/README.md b/README.md
index abe0d4e..edc54ae 100644
--- a/README.md
+++ b/README.md
@@ -39,26 +39,19 @@
 > [!NOTE]
 > If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
 
-<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
-     Explain what rows and columns represent. For instance (please edit as appropriate):
-
 First, prepare a samplesheet with your input data that looks as follows:
 
 `samplesheet.csv`:
 
 ```csv
-sample,fastq_1,fastq_2
-CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
+sample,lane,group,fastq_1,fastq_2,rundir
+CONTROL_REP1,1,GROUP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX
 ```
 
 Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
 
--->
-
 Now, you can run the pipeline using:
 
-<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->
-
 ```bash
 nextflow run nf-core/seqinspector \
    -profile <docker/singularity/.../institute> \

From df4e9cbcbd1f62990f44dd90d9eb0a2990d0c657 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Tue, 14 May 2024 12:43:27 +0200
Subject: [PATCH 26/58] Run prettier

---
 docs/output.md | 2 --
 1 file changed, 2 deletions(-)

diff --git a/docs/output.md b/docs/output.md
index f83e1fa..7af7806 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -68,10 +68,8 @@ The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They m
     - `RUNDIR2/`
       - ...
 
-
 [1] These files will only be generated if `lane`, `group` or `rundir` were specified for some samples.
 
-
 </details>
 
 [MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory.

From 2303db9a4c28fe0b5a907ab73bc3946f3e3daa3e Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <89784800+kedhammar@users.noreply.github.com>
Date: Thu, 16 May 2024 16:00:32 +0200
Subject: [PATCH 27/58] Use testdata base path param in
 tests/MiSeq.main.nf.test

Co-authored-by: Matthias Zepper <6963520+MatthiasZepper@users.noreply.github.com>
---
 tests/MiSeq.main.nf.test | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/MiSeq.main.nf.test b/tests/MiSeq.main.nf.test
index 1e72de9..a3dc0a5 100644
--- a/tests/MiSeq.main.nf.test
+++ b/tests/MiSeq.main.nf.test
@@ -10,7 +10,7 @@ nextflow_pipeline {
         when {
             params {
                 outdir = "$outputDir"
-                input  = "https://raw.githubusercontent.com/nf-core/test-datasets/seqinspector/testdata/MiSeq/samplesheet.csv"
+                input  = params.pipelines_testdata_base_path + "seqinspector/testdata/MiSeq/samplesheet.csv"
             }
         }
 

From 1ea8ac0dac6c0cb11e098beb3c516ba0bb6cdc49 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <89784800+kedhammar@users.noreply.github.com>
Date: Thu, 16 May 2024 16:01:00 +0200
Subject: [PATCH 28/58] Use testdata base path param in
 tests/NovaSeq6000.main.nf.test

Co-authored-by: Matthias Zepper <6963520+MatthiasZepper@users.noreply.github.com>
---
 tests/NovaSeq6000.main.nf.test | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/NovaSeq6000.main.nf.test b/tests/NovaSeq6000.main.nf.test
index f5de9aa..bc687ab 100644
--- a/tests/NovaSeq6000.main.nf.test
+++ b/tests/NovaSeq6000.main.nf.test
@@ -10,7 +10,7 @@ nextflow_pipeline {
         when {
             params {
                 outdir = "$outputDir"
-                input  = "https://raw.githubusercontent.com/nf-core/test-datasets/seqinspector/testdata/NovaSeq6000/samplesheet.csv"
+                input  = params.pipelines_testdata_base_path + "seqinspector/testdata/NovaSeq6000/samplesheet.csv"
             }
         }
 

From 048765fd18409769442915dcd403da682dfd852f Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <89784800+kedhammar@users.noreply.github.com>
Date: Thu, 16 May 2024 16:01:20 +0200
Subject: [PATCH 29/58] Use testdata base path param in
 tests/PromethION.main.nf.test

Co-authored-by: Matthias Zepper <6963520+MatthiasZepper@users.noreply.github.com>
---
 tests/PromethION.main.nf.test | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/PromethION.main.nf.test b/tests/PromethION.main.nf.test
index de2beb3..d1969f3 100644
--- a/tests/PromethION.main.nf.test
+++ b/tests/PromethION.main.nf.test
@@ -10,7 +10,7 @@ nextflow_pipeline {
         when {
             params {
                 outdir = "$outputDir"
-                input  = "https://raw.githubusercontent.com/nf-core/test-datasets/seqinspector/testdata/PromethION/samplesheet.csv"
+                input  = params.pipelines_testdata_base_path + "seqinspector/testdata/PromethION/samplesheet.csv"
             }
         }
 

From 4329bb97c229bcb4d869e3c2d88af08cab730b37 Mon Sep 17 00:00:00 2001
From: Matthias Zepper <MatthiasZepper@users.noreply.github.com>
Date: Fri, 17 May 2024 11:38:29 +0200
Subject: [PATCH 30/58] Make the tests work with 'pipelines_testdata_base_path'
 parameter.

---
 tests/MiSeq.main.nf.test              | 2 +-
 tests/MiSeq.main.nf.test.config       | 7 +++++++
 tests/NovaSeq6000.main.nf.test        | 2 +-
 tests/NovaSeq6000.main.nf.test.config | 7 +++++++
 tests/PromethION.main.nf.test         | 2 +-
 tests/PromethION.main.nf.test.config  | 7 +++++++
 tests/nextflow.config                 | 5 +++++
 7 files changed, 29 insertions(+), 3 deletions(-)
 create mode 100644 tests/MiSeq.main.nf.test.config
 create mode 100644 tests/NovaSeq6000.main.nf.test.config
 create mode 100644 tests/PromethION.main.nf.test.config

diff --git a/tests/MiSeq.main.nf.test b/tests/MiSeq.main.nf.test
index a3dc0a5..bfabd95 100644
--- a/tests/MiSeq.main.nf.test
+++ b/tests/MiSeq.main.nf.test
@@ -8,9 +8,9 @@ nextflow_pipeline {
     test("MiSeq data test") {
 
         when {
+            config "./MiSeq.main.nf.test.config"
             params {
                 outdir = "$outputDir"
-                input  = params.pipelines_testdata_base_path + "seqinspector/testdata/MiSeq/samplesheet.csv"
             }
         }
 
diff --git a/tests/MiSeq.main.nf.test.config b/tests/MiSeq.main.nf.test.config
new file mode 100644
index 0000000..073a977
--- /dev/null
+++ b/tests/MiSeq.main.nf.test.config
@@ -0,0 +1,7 @@
+// Load the basic test config
+includeConfig 'nextflow.config'
+
+// Load the correct samplesheet for that test
+params {
+    input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/MiSeq/samplesheet.csv'
+}
diff --git a/tests/NovaSeq6000.main.nf.test b/tests/NovaSeq6000.main.nf.test
index bc687ab..174e215 100644
--- a/tests/NovaSeq6000.main.nf.test
+++ b/tests/NovaSeq6000.main.nf.test
@@ -8,9 +8,9 @@ nextflow_pipeline {
     test("NovaSeq6000 data test") {
 
         when {
+            config "./NovaSeq6000.main.nf.test.config"
             params {
                 outdir = "$outputDir"
-                input  = params.pipelines_testdata_base_path + "seqinspector/testdata/NovaSeq6000/samplesheet.csv"
             }
         }
 
diff --git a/tests/NovaSeq6000.main.nf.test.config b/tests/NovaSeq6000.main.nf.test.config
new file mode 100644
index 0000000..cad5edd
--- /dev/null
+++ b/tests/NovaSeq6000.main.nf.test.config
@@ -0,0 +1,7 @@
+// Load the basic test config
+includeConfig 'nextflow.config'
+
+// Load the correct samplesheet for that test
+params {
+    input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/NovaSeq6000/samplesheet.csv'
+}
diff --git a/tests/PromethION.main.nf.test b/tests/PromethION.main.nf.test
index d1969f3..3928478 100644
--- a/tests/PromethION.main.nf.test
+++ b/tests/PromethION.main.nf.test
@@ -8,9 +8,9 @@ nextflow_pipeline {
     test("PromethION data test") {
 
         when {
+            config "./PromethION.main.nf.test.config"
             params {
                 outdir = "$outputDir"
-                input  = params.pipelines_testdata_base_path + "seqinspector/testdata/PromethION/samplesheet.csv"
             }
         }
 
diff --git a/tests/PromethION.main.nf.test.config b/tests/PromethION.main.nf.test.config
new file mode 100644
index 0000000..e1498a4
--- /dev/null
+++ b/tests/PromethION.main.nf.test.config
@@ -0,0 +1,7 @@
+// Load the basic test config
+includeConfig 'nextflow.config'
+
+// Load the correct samplesheet for that test
+params {
+    input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/PromethION/samplesheet.csv'
+}
diff --git a/tests/nextflow.config b/tests/nextflow.config
index 422545b..8d9ef46 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -13,4 +13,9 @@ params {
     max_memory = '3.GB'
     max_time   = '2.h'
 
+    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
+
+    validationSchemaIgnoreParams = 'genomes,igenomes_base,pipelines_testdata_base_path'
+
+
 }

From 3ff850395b52b9ee509901f203c301fd40aa9844 Mon Sep 17 00:00:00 2001
From: kedhammar <alfred.kedhammar@scilifelab.se>
Date: Fri, 17 May 2024 13:28:56 +0200
Subject: [PATCH 31/58] update snapshots, add nf-test.log to gitignore

---
 .gitignore                          |  1 +
 tests/MiSeq.main.nf.test.snap       | 12 ++++++++----
 tests/NovaSeq6000.main.nf.test.snap | 18 +++++++++++-------
 tests/PromethION.main.nf.test.snap  | 10 +++++++---
 4 files changed, 27 insertions(+), 14 deletions(-)

diff --git a/.gitignore b/.gitignore
index 089a407..7227765 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,3 +7,4 @@ testing/
 testing*
 *.pyc
 .nf-test
+.nf-test.log
diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index e222b51..9689638 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -4,16 +4,20 @@
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,692b8aed0614ed1655f2c1cbea1ba312",
             "multiqc_general_stats.txt:md5,630167d67d3f92408cd1a04422c7196f",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
+            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,692b8aed0614ed1655f2c1cbea1ba312",
             "multiqc_general_stats.txt:md5,630167d67d3f92408cd1a04422c7196f",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
+            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,692b8aed0614ed1655f2c1cbea1ba312",
             "multiqc_general_stats.txt:md5,630167d67d3f92408cd1a04422c7196f",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95"
+            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921"
         ],
-        "timestamp": "2024-05-08T16:29:33.284003"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-17T12:59:21.531493"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index a406b89..cbb7538 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -4,28 +4,32 @@
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,5ba3f4f4ec6026a5f5d55418384dcd3e",
             "multiqc_general_stats.txt:md5,123cd6b64c9c15607405bcdd45a843d4",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
+            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,9b4fd8a6d6e8a9acabecd592f633472e",
             "multiqc_general_stats.txt:md5,8237b88ceb018d3cb1edcea62d10f4a2",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
+            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,9246a5b6b7b0410c79049fc3dbd08e92",
             "multiqc_general_stats.txt:md5,44328403f423c6f5ac9ee0a8a01e6725",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
+            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,84820276fae52d4d492831280ae6207c",
             "multiqc_general_stats.txt:md5,dd07799e5e4b9d389f9de49a852c3363",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
+            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,59ae05d89453da6f57010ffb6466f902",
             "multiqc_general_stats.txt:md5,e4629691992bfe639c01a84b90563334",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
+            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,5ba3f4f4ec6026a5f5d55418384dcd3e",
             "multiqc_general_stats.txt:md5,123cd6b64c9c15607405bcdd45a843d4",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95"
+            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921"
         ],
-        "timestamp": "2024-05-14T10:17:35.440827"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-17T13:02:20.874181"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index 24e52bd..951c555 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -4,12 +4,16 @@
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,333360ff12007d64f2bf7673b0658bed",
             "multiqc_general_stats.txt:md5,b1999255f9a502618d59be2f2e93bad2",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
+            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,333360ff12007d64f2bf7673b0658bed",
             "multiqc_general_stats.txt:md5,b1999255f9a502618d59be2f2e93bad2",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95"
+            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921"
         ],
-        "timestamp": "2024-05-08T17:17:23.151259"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-17T12:58:02.572837"
     }
 }
\ No newline at end of file

From 8ac4d76770515159a23f746d4d3fa8c4d3e06ce1 Mon Sep 17 00:00:00 2001
From: kedhammar <alfred.kedhammar@scilifelab.se>
Date: Fri, 17 May 2024 15:49:01 +0200
Subject: [PATCH 32/58] visualize example run dir corresponsing to samplesheet

---
 docs/usage.md | 32 +++++++++++++++++++++-----------
 1 file changed, 21 insertions(+), 11 deletions(-)

diff --git a/docs/usage.md b/docs/usage.md
index 5731497..7a4ec73 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -10,7 +10,7 @@
 
 ## Samplesheet input
 
-You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row as shown in the examples below.
+You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location.
 
 ```bash
 --input '[path to samplesheet file]'
@@ -18,15 +18,25 @@ You will need to create a samplesheet with information about the samples you wou
 
 ### Full samplesheet
 
+The following simple run dir structure...
+
+```
+run_dir
+├── sample1_lane1_group1_r1.fq.gz
+├── sample2_lane1_group1_r1.fq.gz
+├── sample3_lane2_group2_r1.fq.gz
+└── sample4_lane2_group3_r1.fq.gz
+```
+
+...would be represented in the following samplesheet (shown as .tsv for readability)
+
 ```csv title="samplesheet.csv"
-sample,lane,group,fastq_1,fastq_2,rundir
-CONTROL_REP1,1,,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX
-CONTROL_REP2,1,,AEG588A2_S2_L002_R1_001.fastq.gz,AEG588A2_S2_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX
-CONTROL_REP3,1,,AEG588A3_S3_L002_R1_001.fastq.gz,AEG588A3_S3_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX
-TREATMENT_REP1,2,GROUP1,AEG588A4_S4_L003_R1_001.fastq.gz,,200624_A00834_0183_BHMTFYDRXX
-TREATMENT_REP2,2,GROUP1,AEG588A5_S5_L003_R1_001.fastq.gz,,200624_A00834_0183_BHMTFYDRXX
-TREATMENT_REP3,2,GROUP2,AEG588A6_S6_L003_R1_001.fastq.gz,,200624_A00834_0183_BHMTFYDRXX
-TREATMENT_REP3,2,GROUP2,AEG588A6_S6_L004_R1_001.fastq.gz,,200624_A00834_0183_BHMTFYDRXX
+sample  lane  group   fastq_1                                       fastq_2 rundir
+sample1 1     group1  path/to/run_dir/sample1_lane1_group1_r1.fq.gz         path/to/run_dir
+sample2 1     group1  path/to/run_dir/sample2_lane1_group1_r1.fq.gz         path/to/run_dir
+sample3 2     group2  path/to/run_dir/sample3_lane2_group2_r1.fq.gz         path/to/run_dir
+sample4 2     group3  path/to/run_dir/sample4_lane2_group3_r1.fq.gz         path/to/run_dir
+
 ```
 
 | Column    | Description                                                                                                                                                                            |
@@ -34,11 +44,11 @@ TREATMENT_REP3,2,GROUP2,AEG588A6_S6_L004_R1_001.fastq.gz,,200624_A00834_0183_BHM
 | `sample`  | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). |
 | `lane`    | Lane where the sample was processed on an Illumina instrument (optional).                                                                                                              |
 | `group`   | Group the sample belongs too, useful when several groups are pooled together (optional).                                                                                               |
-| `rundir`  | Path to the runfolder containing extra information about the sequencing run (optional) .                                                                                               |
 | `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".                                                             |
 | `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz" (optional).                                                  |
+| `rundir`  | Path to the runfolder containing extra information about the sequencing run (optional) .                                                                                               |
 
-An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.
+Another [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.
 
 ## Running the pipeline
 

From 84c9b3d95c693b722a3e61752ba498b05fc08e57 Mon Sep 17 00:00:00 2001
From: kedhammar <alfred.kedhammar@scilifelab.se>
Date: Mon, 20 May 2024 12:41:50 +0200
Subject: [PATCH 33/58] naming fixes

---
 main.nf                   | 4 ++--
 workflows/seqinspector.nf | 9 ++++-----
 2 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/main.nf b/main.nf
index 9de4f94..fb00bd5 100644
--- a/main.nf
+++ b/main.nf
@@ -59,8 +59,8 @@ workflow NFCORE_SEQINSPECTOR {
 
     emit:
     global_report = SEQINSPECTOR.out.global_report  // channel: /path/to/multiqc_report.html
-    lane_reports = SEQINSPECTOR.out.lane_reports    // channel: /path/to/multiqc_report.html
-    group_report = SEQINSPECTOR.out.group_reports   // channel: /path/to/multiqc_report.html
+    lane_reports  = SEQINSPECTOR.out.lane_reports   // channel: /path/to/multiqc_report.html
+    group_reports = SEQINSPECTOR.out.group_reports  // channel: /path/to/multiqc_report.html
     rundir_report = SEQINSPECTOR.out.rundir_reports // channel: /path/to/multiqc_report.html
 
 }
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 0eb375d..50fa481 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -6,7 +6,7 @@
 
 include { FASTQC                        } from '../modules/nf-core/fastqc/main'
 
-include { MULTIQC                       } from '../modules/nf-core/multiqc/main'
+include { MULTIQC as MULTIQC_GLOBAL     } from '../modules/nf-core/multiqc/main'
 include { MULTIQC as MULTIQC_PER_LANE   } from '../modules/nf-core/multiqc/main'
 include { MULTIQC as MULTIQC_PER_GROUP  } from '../modules/nf-core/multiqc/main'
 include { MULTIQC as MULTIQC_PER_RUNDIR } from '../modules/nf-core/multiqc/main'
@@ -84,7 +84,7 @@ workflow SEQINSPECTOR {
         )
     )
 
-    MULTIQC (
+    MULTIQC_GLOBAL (
         ch_multiqc_files
             .map { meta, file -> file }
             .mix(ch_multiqc_extra_files)
@@ -97,9 +97,8 @@ workflow SEQINSPECTOR {
     // Generate reports by lane
     multiqc_extra_files_per_lane = ch_multiqc_files
         .filter { meta, sample -> meta.lane }
-        .map { meta, sample -> meta.lane }
+        .map { meta, sample -> [lane: meta.lane] }
         .unique()
-        .map { lane -> [lane:lane] }
         .combine(ch_multiqc_extra_files)
 
     lane_mqc_files = ch_multiqc_files
@@ -209,7 +208,7 @@ workflow SEQINSPECTOR {
     )
 
     emit:
-    global_report = MULTIQC.out.report.toList()             // channel: /path/to/multiqc_report.html
+    global_report = MULTIQC_GLOBAL.out.report.toList()      // channel: /path/to/multiqc_report.html
     lane_reports = MULTIQC_PER_LANE.out.report.toList()     // channel: [ /path/to/multiqc_report.html ]
     group_reports = MULTIQC_PER_GROUP.out.report.toList()   // channel: [ /path/to/multiqc_report.html ]
     rundir_reports = MULTIQC_PER_RUNDIR.out.report.toList() // channel: [ /path/to/multiqc_report.html ]

From aaf17b68f90dcaa123a9bc0c7807c7bba0dc2fbd Mon Sep 17 00:00:00 2001
From: kedhammar <alfred.kedhammar@scilifelab.se>
Date: Mon, 20 May 2024 12:44:01 +0200
Subject: [PATCH 34/58] nf-core sync

---
 .github/PULL_REQUEST_TEMPLATE.md      |  2 +-
 .github/workflows/linting.yml         | 19 ++++++++++---------
 .github/workflows/linting_comment.yml |  2 +-
 3 files changed, 12 insertions(+), 11 deletions(-)

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index 6de151f..5d27c53 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/seqi
 - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/seqinspector/tree/master/.github/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/seqinspector _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core lint`).
-- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
+- [ ] Ensure the test suite passes (`nf-test test main.nf.test -profile test,docker`).
 - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 1fcafe8..073e187 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -14,12 +14,13 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
-      - name: Set up Python 3.12
-        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+      - name: Set up Python 3.11
+        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
-          python-version: "3.12"
+          python-version: 3.11
+          cache: "pip"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -31,14 +32,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v2
+        uses: nf-core/setup-nextflow@v1
 
-      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
-          python-version: "3.12"
+          python-version: "3.11"
           architecture: "x64"
 
       - name: Install dependencies
@@ -59,7 +60,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
+        uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
         with:
           name: linting-logs
           path: |
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index 40acc23..b706875 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3
+        uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3
         with:
           workflow: linting.yml
           workflow_conclusion: completed

From e6dfea9ca1fbbb0019e438c6394d62daf1f2cda8 Mon Sep 17 00:00:00 2001
From: kedhammar <alfred.kedhammar@scilifelab.se>
Date: Mon, 20 May 2024 12:44:54 +0200
Subject: [PATCH 35/58] nf-core fixes

---
 .github/PULL_REQUEST_TEMPLATE.md      |  2 +-
 .github/workflows/linting.yml         | 19 +++++++++----------
 .github/workflows/linting_comment.yml |  2 +-
 3 files changed, 11 insertions(+), 12 deletions(-)

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index 5d27c53..6de151f 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/seqi
 - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/seqinspector/tree/master/.github/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/seqinspector _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core lint`).
-- [ ] Ensure the test suite passes (`nf-test test main.nf.test -profile test,docker`).
+- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 073e187..1fcafe8 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -14,13 +14,12 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
-      - name: Set up Python 3.11
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - name: Set up Python 3.12
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: 3.11
-          cache: "pip"
+          python-version: "3.12"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -32,14 +31,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           architecture: "x64"
 
       - name: Install dependencies
@@ -60,7 +59,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
+        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
         with:
           name: linting-logs
           path: |
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index b706875..40acc23 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3
+        uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3
         with:
           workflow: linting.yml
           workflow_conclusion: completed

From 02affeb602655023888b330b0402bcbe2a0e613a Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Thu, 30 May 2024 13:18:36 +0200
Subject: [PATCH 36/58] Improve publishDir logic

---
 conf/modules.config                 | 56 +++++++++++++++++++++++++----
 tests/MiSeq.main.nf.test.snap       | 12 +++----
 tests/NovaSeq6000.main.nf.test.snap | 18 ++++------
 tests/PromethION.main.nf.test.snap  | 10 ++----
 4 files changed, 64 insertions(+), 32 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index da3d2ca..f7e7845 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -22,11 +22,20 @@ process {
         ext.args = '--quiet'
     }
 
-    withName: 'MULTIQC' {
+    withName: 'MULTIQC_GLOBAL' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [
             path: { "${params.outdir}/multiqc" },
             mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: 'MULTIQC_PER_LANE' {
+        ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
+        publishDir = [
+            path: { "${params.outdir}/multiqc/lanes" },
+            mode: params.publish_dir_mode,
             saveAs: {
                 filename ->
                     switch (filename) {
@@ -38,27 +47,62 @@ process {
                             def new_filename = filename.replaceFirst(
                                 "(?<prefix>.*)\\[LANE:${lane}\\]_(?<suffix>multiqc_(report\\.html|plots|data).*)",
                                 '${prefix}${suffix}')
-                            "lanes/L${lane}/${new_filename}"
+                            "L${lane}/${new_filename}"
+                            break
+                        default:
+                            filename
+                    }
+            }
+        ]
+    }
+
+    withName: 'MULTIQC_PER_GROUP' {
+        ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
+        publishDir = [
+            path: { "${params.outdir}/multiqc/groups" },
+            mode: params.publish_dir_mode,
+            saveAs: {
+                filename ->
+                    switch (filename) {
+                        case 'versions.yml':
+                            null
                             break
                         case ~/\[GROUP:.+\]_multiqc_(report\.html|plots|data)/:
                             def group = (filename =~ /\[GROUP:(.+)\]_multiqc_(report\.html|plots|data)/)[0][1]
                             def new_filename = filename.replaceFirst(
                                 "(?<prefix>.*)\\[GROUP:${group}\\]_(?<suffix>multiqc_(report\\.html|plots|data).*)",
                                 '${prefix}${suffix}')
-                            "groups/${group}/${new_filename}"
+                            "${group}/${new_filename}"
+                            break
+                        default:
+                            filename
+                    }
+            }
+        ]
+    }
+
+    withName: 'MULTIQC_PER_RUNDIR' {
+        ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
+        publishDir = [
+            path: { "${params.outdir}/multiqc/rundirss" },
+            mode: params.publish_dir_mode,
+            saveAs: {
+                filename ->
+                    switch (filename) {
+                        case 'versions.yml':
+                            null
                             break
                         case ~/\[RUNDIR:.+\]_multiqc_(report\.html|plots|data)/:
                             def rundir = (filename =~ /\[RUNDIR:(.+)\]_multiqc_(report\.html|plots|data)/)[0][1]
                             def new_filename = filename.replaceFirst(
                                 "(?<prefix>.*)\\[RUNDIR:${rundir}\\]_(?<suffix>multiqc_(report\\.html|plots|data).*)",
                                 '${prefix}${suffix}')
-                            "rundirs/${rundir}/${new_filename}"
+                            "${rundir}/${new_filename}"
                             break
                         default:
                             filename
-                }
+                    }
             }
         ]
     }
-
 }
diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index 9689638..87c1a56 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -4,20 +4,16 @@
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,692b8aed0614ed1655f2c1cbea1ba312",
             "multiqc_general_stats.txt:md5,630167d67d3f92408cd1a04422c7196f",
-            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921",
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,692b8aed0614ed1655f2c1cbea1ba312",
             "multiqc_general_stats.txt:md5,630167d67d3f92408cd1a04422c7196f",
-            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921",
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,692b8aed0614ed1655f2c1cbea1ba312",
             "multiqc_general_stats.txt:md5,630167d67d3f92408cd1a04422c7196f",
-            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921"
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95"
         ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-05-17T12:59:21.531493"
+        "timestamp": "2024-05-30T13:14:20.263485"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index cbb7538..2260025 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -4,32 +4,28 @@
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,5ba3f4f4ec6026a5f5d55418384dcd3e",
             "multiqc_general_stats.txt:md5,123cd6b64c9c15607405bcdd45a843d4",
-            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921",
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,9b4fd8a6d6e8a9acabecd592f633472e",
             "multiqc_general_stats.txt:md5,8237b88ceb018d3cb1edcea62d10f4a2",
-            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921",
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,9246a5b6b7b0410c79049fc3dbd08e92",
             "multiqc_general_stats.txt:md5,44328403f423c6f5ac9ee0a8a01e6725",
-            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921",
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,84820276fae52d4d492831280ae6207c",
             "multiqc_general_stats.txt:md5,dd07799e5e4b9d389f9de49a852c3363",
-            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921",
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,59ae05d89453da6f57010ffb6466f902",
             "multiqc_general_stats.txt:md5,e4629691992bfe639c01a84b90563334",
-            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921",
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,5ba3f4f4ec6026a5f5d55418384dcd3e",
             "multiqc_general_stats.txt:md5,123cd6b64c9c15607405bcdd45a843d4",
-            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921"
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95"
         ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-05-17T13:02:20.874181"
+        "timestamp": "2024-05-30T13:13:49.062282"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index 951c555..0ac213c 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -4,16 +4,12 @@
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,333360ff12007d64f2bf7673b0658bed",
             "multiqc_general_stats.txt:md5,b1999255f9a502618d59be2f2e93bad2",
-            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921",
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,333360ff12007d64f2bf7673b0658bed",
             "multiqc_general_stats.txt:md5,b1999255f9a502618d59be2f2e93bad2",
-            "multiqc_software_versions.txt:md5,b1e01403f9bdaa81ebabd388d5f9a921"
+            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95"
         ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-05-17T12:58:02.572837"
+        "timestamp": "2024-05-30T13:14:40.99246"
     }
 }
\ No newline at end of file

From 8b83f13f95c26d7f336d53fc4f9571c14ab3b247 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Tue, 27 Aug 2024 13:17:02 +0200
Subject: [PATCH 37/58] Implement tagging system

---
 README.md                                     |   4 +-
 assets/samplesheet.csv                        |  10 +-
 assets/schema_input.json                      |  16 +--
 conf/modules.config                           |  64 +--------
 docs/output.md                                |  45 +++---
 docs/usage.md                                 |  13 +-
 main.nf                                       |   6 +-
 .../main.nf                                   |   4 +-
 tests/MiSeq.main.nf.test                      |  18 +--
 tests/MiSeq.main.nf.test.snap                 |  14 +-
 tests/NovaSeq6000.main.nf.test                |  53 ++++---
 tests/NovaSeq6000.main.nf.test.snap           |  26 ++--
 tests/PromethION.main.nf.test                 |  13 +-
 tests/PromethION.main.nf.test.snap            |  10 +-
 workflows/seqinspector.nf                     | 131 ++++--------------
 15 files changed, 126 insertions(+), 301 deletions(-)

diff --git a/README.md b/README.md
index 7efdd3e..31018e7 100644
--- a/README.md
+++ b/README.md
@@ -44,8 +44,8 @@ First, prepare a samplesheet with your input data that looks as follows:
 `samplesheet.csv`:
 
 ```csv
-sample,lane,group,fastq_1,fastq_2,rundir
-CONTROL_REP1,1,GROUP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX
+sample,fastq_1,fastq_2,rundir,tags
+CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,"patient1"
 ```
 
 Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv
index fef3b4e..00019e5 100644
--- a/assets/samplesheet.csv
+++ b/assets/samplesheet.csv
@@ -1,3 +1,7 @@
-sample,lane,group,fastq_1,fastq_2,rundir
-SAMPLE_PAIRED_END,1,P001,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz,/path/to/rundir
-SAMPLE_SINGLE_END,2,P002,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,/path/to/rundir
+sample,fastq_1,fastq_2,rundir,tags
+SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz,/path/to/rundir,"paired_sample,cohort1"
+SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A2_S2_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A2_S2_L002_R2_001.fastq.gz,/path/to/rundir,"paired_sample,cohort1"
+SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A3_S3_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A3_S3_L002_R2_001.fastq.gz,/path/to/rundir,"paired_sample,cohort2"
+SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,/path/to/rundir,"patient1"
+SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,/path/to/rundir,"patient2"
+SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,/path/to/rundir,"patient3"
diff --git a/assets/schema_input.json b/assets/schema_input.json
index c9800d5..62922b7 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -13,18 +13,6 @@
                 "errorMessage": "Sample name must be provided and cannot contain spaces",
                 "meta": ["sample"]
             },
-            "lane": {
-                "type": "integer",
-                "pattern": "^\\d+$",
-                "errorMessage": "Lane ID must be a number",
-                "meta": ["lane"]
-            },
-            "group": {
-                "type": "string",
-                "pattern": "^\\S+$",
-                "errorMessage": "Group ID cannot contain spaces",
-                "meta": ["group"]
-            },
             "fastq_1": {
                 "type": "string",
                 "format": "file-path",
@@ -45,6 +33,10 @@
                 "exists": true,
                 "errorMessage": "Run directory must be a path",
                 "meta": ["rundir"]
+            },
+            "tags": {
+                "type": "string",
+                "meta": ["tags"]
             }
         },
         "required": ["sample", "fastq_1"],
diff --git a/conf/modules.config b/conf/modules.config
index f7e7845..c883822 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -25,16 +25,16 @@ process {
     withName: 'MULTIQC_GLOBAL' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [
-            path: { "${params.outdir}/multiqc" },
+            path: { "${params.outdir}/multiqc/global_report" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
-    withName: 'MULTIQC_PER_LANE' {
+    withName: 'MULTIQC_PER_TAG' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [
-            path: { "${params.outdir}/multiqc/lanes" },
+            path: { "${params.outdir}/multiqc/group_reports" },
             mode: params.publish_dir_mode,
             saveAs: {
                 filename ->
@@ -42,62 +42,12 @@ process {
                         case 'versions.yml':
                             null
                             break
-                        case ~/\[LANE:\d+\]_multiqc_(report\.html|plots|data)/:
-                            def lane = (filename =~ /\[LANE:(\d+)\]_multiqc_(report\.html|plots|data)/)[0][1]
+                        case ~/\[TAG:.+\]_multiqc_(report\.html|plots|data)/:
+                            def tag = (filename =~ /\[TAG:(.+)\]_multiqc_(report\.html|plots|data)/)[0][1]
                             def new_filename = filename.replaceFirst(
-                                "(?<prefix>.*)\\[LANE:${lane}\\]_(?<suffix>multiqc_(report\\.html|plots|data).*)",
+                                "(?<prefix>.*)\\[TAG:${tag}\\]_(?<suffix>multiqc_(report\\.html|plots|data).*)",
                                 '${prefix}${suffix}')
-                            "L${lane}/${new_filename}"
-                            break
-                        default:
-                            filename
-                    }
-            }
-        ]
-    }
-
-    withName: 'MULTIQC_PER_GROUP' {
-        ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
-        publishDir = [
-            path: { "${params.outdir}/multiqc/groups" },
-            mode: params.publish_dir_mode,
-            saveAs: {
-                filename ->
-                    switch (filename) {
-                        case 'versions.yml':
-                            null
-                            break
-                        case ~/\[GROUP:.+\]_multiqc_(report\.html|plots|data)/:
-                            def group = (filename =~ /\[GROUP:(.+)\]_multiqc_(report\.html|plots|data)/)[0][1]
-                            def new_filename = filename.replaceFirst(
-                                "(?<prefix>.*)\\[GROUP:${group}\\]_(?<suffix>multiqc_(report\\.html|plots|data).*)",
-                                '${prefix}${suffix}')
-                            "${group}/${new_filename}"
-                            break
-                        default:
-                            filename
-                    }
-            }
-        ]
-    }
-
-    withName: 'MULTIQC_PER_RUNDIR' {
-        ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
-        publishDir = [
-            path: { "${params.outdir}/multiqc/rundirss" },
-            mode: params.publish_dir_mode,
-            saveAs: {
-                filename ->
-                    switch (filename) {
-                        case 'versions.yml':
-                            null
-                            break
-                        case ~/\[RUNDIR:.+\]_multiqc_(report\.html|plots|data)/:
-                            def rundir = (filename =~ /\[RUNDIR:(.+)\]_multiqc_(report\.html|plots|data)/)[0][1]
-                            def new_filename = filename.replaceFirst(
-                                "(?<prefix>.*)\\[RUNDIR:${rundir}\\]_(?<suffix>multiqc_(report\\.html|plots|data).*)",
-                                '${prefix}${suffix}')
-                            "${rundir}/${new_filename}"
+                            "${tag}/${new_filename}"
                             break
                         default:
                             filename
diff --git a/docs/output.md b/docs/output.md
index 7af7806..15c29ce 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -39,36 +39,29 @@ The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They m
 
 ### MultiQC
 
+nf-core/seqinspector will generate the following MultiQC reports:
+
+- one global reports including all the samples listed in the samplesheet
+- one group report per unique tag. These reports compile samples that share the same tag.
+
 <details markdown="1">
 <summary>Output files</summary>
 
 - `multiqc/`
-  - `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser.
-  - `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline.
-  - `multiqc_plots/`: directory containing static images from the report in various formats.
-  - `lanes/` [1]
-    - `L1/`
-      - `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser.
-      - `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline.
-      - `multiqc_plots/`: directory containing static images from the report in various formats.
-    - `L2/`
-      - ...
-  - `groups/` [1]
-    - `GROUPNAME1/`
-      - `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser.
-      - `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline.
-      - `multiqc_plots/`: directory containing static images from the report in various formats.
-    - `GROUPNAME2/`
-      - ...
-  - `rundir/` [1]
-    - `RUNDIR1/`
-      - `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser.
-      - `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline.
-      - `multiqc_plots/`: directory containing static images from the report in various formats.
-    - `RUNDIR2/`
-      - ...
-
-[1] These files will only be generated if `lane`, `group` or `rundir` were specified for some samples.
+  - `global_report`
+    - `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser.
+    - `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline.
+    - `multiqc_plots/`: directory containing static images from the report in various formats.
+  - `group_reports`
+    - `tag1/`
+      - `multiqc_report.html`
+      - `multiqc_data/`
+      - `multiqc_plots/`
+    - `tag2/`
+      - `multiqc_report.html`
+      - `multiqc_data/`
+      - `multiqc_plots/`
+    - ...
 
 </details>
 
diff --git a/docs/usage.md b/docs/usage.md
index 7a4ec73..42d596b 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -31,22 +31,21 @@ run_dir
 ...would be represented in the following samplesheet (shown as .tsv for readability)
 
 ```csv title="samplesheet.csv"
-sample  lane  group   fastq_1                                       fastq_2 rundir
-sample1 1     group1  path/to/run_dir/sample1_lane1_group1_r1.fq.gz         path/to/run_dir
-sample2 1     group1  path/to/run_dir/sample2_lane1_group1_r1.fq.gz         path/to/run_dir
-sample3 2     group2  path/to/run_dir/sample3_lane2_group2_r1.fq.gz         path/to/run_dir
-sample4 2     group3  path/to/run_dir/sample4_lane2_group3_r1.fq.gz         path/to/run_dir
+sample  fastq_1                                       fastq_2 rundir          tags
+sample1 path/to/run_dir/sample1_lane1_group1_r1.fq.gz         path/to/run_dir "cohort1,patient1"
+sample2 path/to/run_dir/sample2_lane1_group1_r1.fq.gz         path/to/run_dir "cohort1,patient2"
+sample3 path/to/run_dir/sample3_lane2_group2_r1.fq.gz         path/to/run_dir "cohort1,patient3"
+sample4 path/to/run_dir/sample4_lane2_group3_r1.fq.gz         path/to/run_dir "control"
 
 ```
 
 | Column    | Description                                                                                                                                                                            |
 | --------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | `sample`  | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). |
-| `lane`    | Lane where the sample was processed on an Illumina instrument (optional).                                                                                                              |
-| `group`   | Group the sample belongs too, useful when several groups are pooled together (optional).                                                                                               |
 | `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".                                                             |
 | `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz" (optional).                                                  |
 | `rundir`  | Path to the runfolder containing extra information about the sequencing run (optional) .                                                                                               |
+| `tags`    | Comma-separated list of tags to group samples in special reports.                                                                                                                      |
 
 Another [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.
 
diff --git a/main.nf b/main.nf
index fb00bd5..a55408e 100644
--- a/main.nf
+++ b/main.nf
@@ -58,10 +58,8 @@ workflow NFCORE_SEQINSPECTOR {
     )
 
     emit:
-    global_report = SEQINSPECTOR.out.global_report  // channel: /path/to/multiqc_report.html
-    lane_reports  = SEQINSPECTOR.out.lane_reports   // channel: /path/to/multiqc_report.html
-    group_reports = SEQINSPECTOR.out.group_reports  // channel: /path/to/multiqc_report.html
-    rundir_report = SEQINSPECTOR.out.rundir_reports // channel: /path/to/multiqc_report.html
+    global_report   = SEQINSPECTOR.out.global_report    // channel: /path/to/multiqc_report.html
+    grouped_reports = SEQINSPECTOR.out.grouped_reports  // channel: /path/to/multiqc_report.html
 
 }
 /*
diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index ea9c9b8..afcfc68 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -84,8 +84,8 @@ workflow PIPELINE_INITIALISATION {
         .fromSamplesheet("input") // Validates samplesheet against $projectDir/assets/schema_input.json. Path to validation schema is defined by $projectDir/nextflow_schema.json
         .map {
             meta, fastq_1, fastq_2 ->
-                def id_string = "${meta.sample}_${meta.group ?: "ungrouped"}_${meta.lane}"
-                def updated_meta = meta + [ id: id_string ]
+                def tags = meta.tags ? meta.tags.tokenize(",") : []
+                def updated_meta = meta + [ id:meta.sample, tags:tags ]
                 if (!fastq_2) {
                     return [ updated_meta.id, updated_meta + [ single_end:true ], [ fastq_1 ] ]
                 } else {
diff --git a/tests/MiSeq.main.nf.test b/tests/MiSeq.main.nf.test
index bfabd95..8fbff4a 100644
--- a/tests/MiSeq.main.nf.test
+++ b/tests/MiSeq.main.nf.test
@@ -18,20 +18,10 @@ nextflow_pipeline {
             assertAll(
                 { assert workflow.success },
                 { assert snapshot(
-                    path("$outputDir/multiqc/lanes/L1/multiqc_data/multiqc_citations.txt"),
-                    path("$outputDir/multiqc/lanes/L1/multiqc_data/multiqc_fastqc.txt"),
-                    path("$outputDir/multiqc/lanes/L1/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/lanes/L1/multiqc_data/multiqc_software_versions.txt"),
-
-                    path("$outputDir/multiqc/groups/P001/multiqc_data/multiqc_citations.txt"),
-                    path("$outputDir/multiqc/groups/P001/multiqc_data/multiqc_fastqc.txt"),
-                    path("$outputDir/multiqc/groups/P001/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/groups/P001/multiqc_data/multiqc_software_versions.txt"),
-
-                    path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"),
-                    path("$outputDir/multiqc/multiqc_data/multiqc_fastqc.txt"),
-                    path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/multiqc_data/multiqc_software_versions.txt"),
+                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_software_versions.txt"),
                     ).match()
                 }
             )
diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index 87c1a56..26f0c2a 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -2,18 +2,10 @@
     "MiSeq data test": {
         "content": [
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,692b8aed0614ed1655f2c1cbea1ba312",
-            "multiqc_general_stats.txt:md5,630167d67d3f92408cd1a04422c7196f",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
-            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,692b8aed0614ed1655f2c1cbea1ba312",
-            "multiqc_general_stats.txt:md5,630167d67d3f92408cd1a04422c7196f",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
-            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,692b8aed0614ed1655f2c1cbea1ba312",
-            "multiqc_general_stats.txt:md5,630167d67d3f92408cd1a04422c7196f",
+            "multiqc_fastqc.txt:md5,e46e7baa8f57d4cf54d973925b5eadf9",
+            "multiqc_general_stats.txt:md5,a5e626a2e1a3c986092e4f89091cc41c",
             "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95"
         ],
-        "timestamp": "2024-05-30T13:14:20.263485"
+        "timestamp": "2024-08-26T17:55:16.152573"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test b/tests/NovaSeq6000.main.nf.test
index 174e215..f93891b 100644
--- a/tests/NovaSeq6000.main.nf.test
+++ b/tests/NovaSeq6000.main.nf.test
@@ -18,35 +18,30 @@ nextflow_pipeline {
             assertAll(
                 { assert workflow.success },
                 { assert snapshot(
-                    path("$outputDir/multiqc/lanes/L1/multiqc_data/multiqc_citations.txt"),
-                    path("$outputDir/multiqc/lanes/L1/multiqc_data/multiqc_fastqc.txt"),
-                    path("$outputDir/multiqc/lanes/L1/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/lanes/L1/multiqc_data/multiqc_software_versions.txt"),
-
-                    path("$outputDir/multiqc/groups/S1/multiqc_data/multiqc_citations.txt"),
-                    path("$outputDir/multiqc/groups/S1/multiqc_data/multiqc_fastqc.txt"),
-                    path("$outputDir/multiqc/groups/S1/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/groups/S1/multiqc_data/multiqc_software_versions.txt"),
-
-                    path("$outputDir/multiqc/groups/S2/multiqc_data/multiqc_citations.txt"),
-                    path("$outputDir/multiqc/groups/S2/multiqc_data/multiqc_fastqc.txt"),
-                    path("$outputDir/multiqc/groups/S2/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/groups/S2/multiqc_data/multiqc_software_versions.txt"),
-
-                    path("$outputDir/multiqc/groups/S3/multiqc_data/multiqc_citations.txt"),
-                    path("$outputDir/multiqc/groups/S3/multiqc_data/multiqc_fastqc.txt"),
-                    path("$outputDir/multiqc/groups/S3/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/groups/S3/multiqc_data/multiqc_software_versions.txt"),
-
-                    path("$outputDir/multiqc/groups/S4/multiqc_data/multiqc_citations.txt"),
-                    path("$outputDir/multiqc/groups/S4/multiqc_data/multiqc_fastqc.txt"),
-                    path("$outputDir/multiqc/groups/S4/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/groups/S4/multiqc_data/multiqc_software_versions.txt"),
-
-                    path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"),
-                    path("$outputDir/multiqc/multiqc_data/multiqc_fastqc.txt"),
-                    path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/multiqc_data/multiqc_software_versions.txt"),
+                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_software_versions.txt"),
+
+                    path("$outputDir/multiqc/group_reports/cohort1/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/group_reports/cohort1/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/group_reports/cohort1/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/group_reports/cohort1/multiqc_data/multiqc_software_versions.txt"),
+
+                    path("$outputDir/multiqc/group_reports/patient1/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/group_reports/patient1/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/group_reports/patient1/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/group_reports/patient1/multiqc_data/multiqc_software_versions.txt"),
+
+                    path("$outputDir/multiqc/group_reports/patient2/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/group_reports/patient2/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/group_reports/patient2/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/group_reports/patient2/multiqc_data/multiqc_software_versions.txt"),
+
+                    path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_software_versions.txt"),
                     ).match()
                 },
             )
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index 2260025..f5c4776 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -2,30 +2,26 @@
     "NovaSeq6000 data test": {
         "content": [
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,5ba3f4f4ec6026a5f5d55418384dcd3e",
-            "multiqc_general_stats.txt:md5,123cd6b64c9c15607405bcdd45a843d4",
+            "multiqc_fastqc.txt:md5,e8ed6dca928396b8873d24e60ea1a133",
+            "multiqc_general_stats.txt:md5,fd9d46c5b441908cd07e5373d116db17",
             "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,9b4fd8a6d6e8a9acabecd592f633472e",
-            "multiqc_general_stats.txt:md5,8237b88ceb018d3cb1edcea62d10f4a2",
+            "multiqc_fastqc.txt:md5,ff9b31c6024f11a8135456e7ea01fc8f",
+            "multiqc_general_stats.txt:md5,f36bd6e27e92c25be076efea411d3a8e",
             "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,9246a5b6b7b0410c79049fc3dbd08e92",
-            "multiqc_general_stats.txt:md5,44328403f423c6f5ac9ee0a8a01e6725",
+            "multiqc_fastqc.txt:md5,62d51280dcd7634f6bed95ffe0d8dab8",
+            "multiqc_general_stats.txt:md5,2012002b6a057be981a97fcc96142a6c",
             "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,84820276fae52d4d492831280ae6207c",
-            "multiqc_general_stats.txt:md5,dd07799e5e4b9d389f9de49a852c3363",
+            "multiqc_fastqc.txt:md5,63749e803a2d5fc7ecc7cd93fa68df1f",
+            "multiqc_general_stats.txt:md5,656931993032400dea3d441b8b61b4d2",
             "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,59ae05d89453da6f57010ffb6466f902",
-            "multiqc_general_stats.txt:md5,e4629691992bfe639c01a84b90563334",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
-            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,5ba3f4f4ec6026a5f5d55418384dcd3e",
-            "multiqc_general_stats.txt:md5,123cd6b64c9c15607405bcdd45a843d4",
+            "multiqc_fastqc.txt:md5,91cc62e1b4059bdbe4b88affa43378af",
+            "multiqc_general_stats.txt:md5,6e500f82550e00b07c3e7aa1d46ab9e9",
             "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95"
         ],
-        "timestamp": "2024-05-30T13:13:49.062282"
+        "timestamp": "2024-08-26T18:03:33.089142"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test b/tests/PromethION.main.nf.test
index 3928478..8fec8b3 100644
--- a/tests/PromethION.main.nf.test
+++ b/tests/PromethION.main.nf.test
@@ -18,15 +18,10 @@ nextflow_pipeline {
             assertAll(
                 { assert workflow.success },
                 { assert snapshot(
-                    path("$outputDir/multiqc/groups/r10p41_e8p2_human_runs_jkw/multiqc_data/multiqc_citations.txt"),
-                    path("$outputDir/multiqc/groups/r10p41_e8p2_human_runs_jkw/multiqc_data/multiqc_fastqc.txt"),
-                    path("$outputDir/multiqc/groups/r10p41_e8p2_human_runs_jkw/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/groups/r10p41_e8p2_human_runs_jkw/multiqc_data/multiqc_software_versions.txt"),
-
-                    path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"),
-                    path("$outputDir/multiqc/multiqc_data/multiqc_fastqc.txt"),
-                    path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/multiqc_data/multiqc_software_versions.txt"),
+                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_software_versions.txt"),
                     ).match()
                 },
             )
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index 0ac213c..e3b34f2 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -2,14 +2,10 @@
     "PromethION data test": {
         "content": [
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,333360ff12007d64f2bf7673b0658bed",
-            "multiqc_general_stats.txt:md5,b1999255f9a502618d59be2f2e93bad2",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
-            "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,333360ff12007d64f2bf7673b0658bed",
-            "multiqc_general_stats.txt:md5,b1999255f9a502618d59be2f2e93bad2",
+            "multiqc_fastqc.txt:md5,cecee3cb343c75c80180d3169c6f3ea1",
+            "multiqc_general_stats.txt:md5,e63c25089c4fc10618414ba2254d18c7",
             "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95"
         ],
-        "timestamp": "2024-05-30T13:14:40.99246"
+        "timestamp": "2024-08-26T17:55:38.755385"
     }
 }
\ No newline at end of file
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 50fa481..e37df50 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -7,9 +7,7 @@
 include { FASTQC                        } from '../modules/nf-core/fastqc/main'
 
 include { MULTIQC as MULTIQC_GLOBAL     } from '../modules/nf-core/multiqc/main'
-include { MULTIQC as MULTIQC_PER_LANE   } from '../modules/nf-core/multiqc/main'
-include { MULTIQC as MULTIQC_PER_GROUP  } from '../modules/nf-core/multiqc/main'
-include { MULTIQC as MULTIQC_PER_RUNDIR } from '../modules/nf-core/multiqc/main'
+include { MULTIQC as MULTIQC_PER_TAG    } from '../modules/nf-core/multiqc/main'
 
 include { paramsSummaryMap              } from 'plugin/nf-validation'
 include { paramsSummaryMultiqc          } from '../subworkflows/nf-core/utils_nfcore_pipeline'
@@ -94,124 +92,51 @@ workflow SEQINSPECTOR {
         ch_multiqc_logo.toList()
     )
 
-    // Generate reports by lane
-    multiqc_extra_files_per_lane = ch_multiqc_files
-        .filter { meta, sample -> meta.lane }
-        .map { meta, sample -> [lane: meta.lane] }
+    ch_tags = ch_multiqc_files
+        .map { meta, sample -> meta.tags }
+        .flatten()
         .unique()
-        .combine(ch_multiqc_extra_files)
 
-    lane_mqc_files = ch_multiqc_files
-        .filter { meta, sample -> meta.lane }
-        .mix(multiqc_extra_files_per_lane)
-        .map { meta, sample -> [ "[LANE:${meta.lane}]", meta, sample ] }
-        .groupTuple()
-        .tap { mqc_by_lane }
-        .collectFile{
-            lane, meta, samples -> [
-                "${lane}_multiqc_extra_config.yml",
-                """
-                    |output_fn_name: \"${lane}_multiqc_report.html\"
-                    |data_dir_name:  \"${lane}_multiqc_data\"
-                    |plots_dir_name: \"${lane}_multiqc_plots\"
-                """.stripMargin()
-            ]
-        }
-        .map { file -> [ (file =~ /(\[LANE:.+\])/)[0][1], file ] }
-        .join(mqc_by_lane)
-        .multiMap { lane, config, meta , samples_per_lane ->
-            samples_per_lane: samples_per_lane
-            config: config
-        }
-
-    MULTIQC_PER_LANE(
-        lane_mqc_files.samples_per_lane,
-        ch_multiqc_config.toList(),
-        lane_mqc_files.config,
-        ch_multiqc_logo.toList()
-    )
-
-    // Generate reports by group
-    multiqc_extra_files_per_group = ch_multiqc_files
-        .filter { meta, sample -> meta.group }
-        .map { meta, sample -> meta.group }
-        .unique()
-        .map { group -> [group:group] }
-        .combine(ch_multiqc_extra_files)
-
-    group_mqc_files = ch_multiqc_files
-        .filter { meta, sample -> meta.group }
-        .mix(multiqc_extra_files_per_group)
-        .map { meta, sample -> [ "[GROUP:${meta.group}]", meta, sample ] }
-        .groupTuple()
-        .tap { mqc_by_group }
-        .collectFile{
-            group, meta, samples -> [
-                "${group}_multiqc_extra_config.yml",
-                """
-                    |output_fn_name: \"${group}_multiqc_report.html\"
-                    |data_dir_name:  \"${group}_multiqc_data\"
-                    |plots_dir_name: \"${group}_multiqc_plots\"
-                """.stripMargin()
-            ]
-        }
-        .map { file -> [ (file =~ /(\[GROUP:.+\])/)[0][1], file ] }
-        .join(mqc_by_group)
-        .multiMap { group, config, meta , samples_per_group ->
-            samples_per_group: samples_per_group
-            config: config
-        }
-
-    MULTIQC_PER_GROUP(
-        group_mqc_files.samples_per_group,
-        ch_multiqc_config.toList(),
-        group_mqc_files.config,
-        ch_multiqc_logo.toList()
-    )
-
-    // Generate reports by rundir
-    multiqc_extra_files_per_rundir = ch_multiqc_files
-        .filter { meta, sample -> meta.rundir }
-        .map { meta, sample -> meta.rundir }
-        .unique()
-        .map { rundir -> [rundir:rundir] }
+    multiqc_extra_files_per_tag = ch_tags
         .combine(ch_multiqc_extra_files)
 
-    rundir_mqc_files = ch_multiqc_files
-        .filter { meta, sample -> meta.rundir }
-        .mix(multiqc_extra_files_per_rundir)
-        .map { meta, sample -> [ "[RUNDIR:${meta.rundir.name}]", meta, sample ] }
+    // Group samples by tag
+    tagged_mqc_files = ch_tags
+        .combine(ch_multiqc_files)
+        .filter { sample_tag, meta, sample -> sample_tag in meta.tags }
+        .map { sample_tag, meta, sample -> [sample_tag, sample] }
+        .mix(multiqc_extra_files_per_tag)
         .groupTuple()
-        .tap { mqc_by_rundir }
-        .collectFile{
-            rundir, meta, samples -> [
-                "${rundir}_multiqc_extra_config.yml",
+        .tap { mqc_by_tag }
+        .collectFile {
+            sample_tag, samples ->
+            def prefix_tag = "[TAG:${sample_tag}]"
+            [
+                "${prefix_tag}_multiqc_extra_config.yml",
                 """
-                    |output_fn_name: \"${rundir}_multiqc_report.html\"
-                    |data_dir_name:  \"${rundir}_multiqc_data\"
-                    |plots_dir_name: \"${rundir}_multiqc_plots\"
+                    |output_fn_name: \"${prefix_tag}_multiqc_report.html\"
+                    |data_dir_name:  \"${prefix_tag}_multiqc_data\"
+                    |plots_dir_name: \"${prefix_tag}_multiqc_plots\"
                 """.stripMargin()
             ]
         }
-        .map { file -> [ (file =~ /(\[RUNDIR:.+\])/)[0][1], file ] }
-        .join(mqc_by_rundir)
-        .multiMap { rundir, config, meta , samples_per_rundir ->
-            samples_per_rundir: samples_per_rundir
+        .map { file -> [ (file =~ /\[TAG:(.+)\]/)[0][1], file ] }
+        .join(mqc_by_tag)
+        .multiMap { sample_tag, config, samples ->
+            samples_per_tag: samples
             config: config
         }
 
-    MULTIQC_PER_RUNDIR(
-        rundir_mqc_files.samples_per_rundir,
+    MULTIQC_PER_TAG(
+        tagged_mqc_files.samples_per_tag,
         ch_multiqc_config.toList(),
-        rundir_mqc_files.config,
+        tagged_mqc_files.config,
         ch_multiqc_logo.toList()
     )
 
     emit:
     global_report = MULTIQC_GLOBAL.out.report.toList()      // channel: /path/to/multiqc_report.html
-    lane_reports = MULTIQC_PER_LANE.out.report.toList()     // channel: [ /path/to/multiqc_report.html ]
-    group_reports = MULTIQC_PER_GROUP.out.report.toList()   // channel: [ /path/to/multiqc_report.html ]
-    rundir_reports = MULTIQC_PER_RUNDIR.out.report.toList() // channel: [ /path/to/multiqc_report.html ]
+    grouped_reports = MULTIQC_PER_TAG.out.report.toList()   // channel: [ /path/to/multiqc_report.html ]
     versions       = ch_versions                            // channel: [ path(versions.yml) ]
 }
 

From dabccc2e556be1860eb990d1914208a8e6901cef Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Tue, 27 Aug 2024 15:08:20 +0200
Subject: [PATCH 38/58] Update changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6430add..3aa5bac 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 
 ### `Added`
 
+- [#20](https://github.com/nf-core/seqinspector/pull/20) Use tags to generate group reports
 - [#13](https://github.com/nf-core/seqinspector/pull/13) Generate reports per run, per project and per lane.
 
 ### `Fixed`

From 8bba88869a4f67143639c61c3972599192140db8 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <89784800+kedhammar@users.noreply.github.com>
Date: Tue, 27 Aug 2024 15:52:46 +0200
Subject: [PATCH 39/58] Try adding regex assertion and error for samplesheet
 tags

---
 assets/schema_input.json | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/assets/schema_input.json b/assets/schema_input.json
index 62922b7..bde27fa 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -36,6 +36,8 @@
             },
             "tags": {
                 "type": "string",
+                "pattern": "^\\\"([A-Za-z0-9_-]+,\\ ?)*([A-Za-z0-9_-]+)\\\"$",
+                "errorMessage": "Tags must consist of numbers, letters, underscores or dashes and must be provided as a comma-separated list flanked by a pair of double-quotes, e.g. \"patient_01, lane1, pos-CTRL_2\"."
                 "meta": ["tags"]
             }
         },

From 6987e93e0e10b39917d56600410db8a61a8f6ec9 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <89784800+kedhammar@users.noreply.github.com>
Date: Tue, 27 Aug 2024 15:55:26 +0200
Subject: [PATCH 40/58] Add missing comma

---
 assets/schema_input.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/assets/schema_input.json b/assets/schema_input.json
index bde27fa..d4a6dc7 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -37,7 +37,7 @@
             "tags": {
                 "type": "string",
                 "pattern": "^\\\"([A-Za-z0-9_-]+,\\ ?)*([A-Za-z0-9_-]+)\\\"$",
-                "errorMessage": "Tags must consist of numbers, letters, underscores or dashes and must be provided as a comma-separated list flanked by a pair of double-quotes, e.g. \"patient_01, lane1, pos-CTRL_2\"."
+                "errorMessage": "Tags must consist of numbers, letters, underscores or dashes and must be provided as a comma-separated list flanked by a pair of double-quotes, e.g. \"patient_01, lane1, pos-CTRL_2\".",
                 "meta": ["tags"]
             }
         },

From 363e782a7a68d2364fd73176eb50d24b72c1c02a Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Tue, 3 Sep 2024 10:35:51 +0200
Subject: [PATCH 41/58] Change example tags to more neutral ones

---
 README.md     | 2 +-
 docs/usage.md | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index 31018e7..679b6f1 100644
--- a/README.md
+++ b/README.md
@@ -45,7 +45,7 @@ First, prepare a samplesheet with your input data that looks as follows:
 
 ```csv
 sample,fastq_1,fastq_2,rundir,tags
-CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,"patient1"
+CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,"group1"
 ```
 
 Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
diff --git a/docs/usage.md b/docs/usage.md
index 42d596b..621c7c0 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -32,9 +32,9 @@ run_dir
 
 ```csv title="samplesheet.csv"
 sample  fastq_1                                       fastq_2 rundir          tags
-sample1 path/to/run_dir/sample1_lane1_group1_r1.fq.gz         path/to/run_dir "cohort1,patient1"
-sample2 path/to/run_dir/sample2_lane1_group1_r1.fq.gz         path/to/run_dir "cohort1,patient2"
-sample3 path/to/run_dir/sample3_lane2_group2_r1.fq.gz         path/to/run_dir "cohort1,patient3"
+sample1 path/to/run_dir/sample1_lane1_group1_r1.fq.gz         path/to/run_dir "project1,group1"
+sample2 path/to/run_dir/sample2_lane1_group1_r1.fq.gz         path/to/run_dir "project1,group1"
+sample3 path/to/run_dir/sample3_lane2_group2_r1.fq.gz         path/to/run_dir "project1,group2"
 sample4 path/to/run_dir/sample4_lane2_group3_r1.fq.gz         path/to/run_dir "control"
 
 ```

From c1a21de429b24fde2f0e5ad8f313f7a7d1b468ba Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Tue, 3 Sep 2024 12:36:42 +0200
Subject: [PATCH 42/58] Check for tag collisions

---
 .../utils_nfcore_seqinspector_pipeline/main.nf     | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index afcfc68..bb875af 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -103,6 +103,20 @@ workflow PIPELINE_INITIALISATION {
         // }
         .set { ch_samplesheet }
 
+    ch_samplesheet
+        .map {
+            meta, fastqs -> meta.tags
+        }
+        .flatten()
+        .unique()
+        .map { tag_name -> [tag_name.toLowerCase(), tag_name] }
+        .groupTuple()
+        .map {
+            tag_lowercase, tags ->
+                assert tags.size() == 1 :
+                "Tag name collision: " + tags.join(", ")
+        }
+
     emit:
     samplesheet = ch_samplesheet
     versions    = ch_versions

From 8a43efa8ae3f78dd846f440b42934e50bba0ab91 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Tue, 3 Sep 2024 12:58:50 +0200
Subject: [PATCH 43/58] Use columns to separate tags

---
 README.md                                     |  2 +-
 assets/samplesheet.csv                        | 12 ++++----
 assets/schema_input.json                      |  4 +--
 docs/usage.md                                 | 10 +++----
 .../main.nf                                   |  2 +-
 tests/NovaSeq6000.main.nf.test                | 28 +++++++++----------
 6 files changed, 29 insertions(+), 29 deletions(-)

diff --git a/README.md b/README.md
index 679b6f1..d7cd233 100644
--- a/README.md
+++ b/README.md
@@ -45,7 +45,7 @@ First, prepare a samplesheet with your input data that looks as follows:
 
 ```csv
 sample,fastq_1,fastq_2,rundir,tags
-CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,"group1"
+CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,group1
 ```
 
 Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv
index 00019e5..ba2542d 100644
--- a/assets/samplesheet.csv
+++ b/assets/samplesheet.csv
@@ -1,7 +1,7 @@
 sample,fastq_1,fastq_2,rundir,tags
-SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz,/path/to/rundir,"paired_sample,cohort1"
-SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A2_S2_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A2_S2_L002_R2_001.fastq.gz,/path/to/rundir,"paired_sample,cohort1"
-SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A3_S3_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A3_S3_L002_R2_001.fastq.gz,/path/to/rundir,"paired_sample,cohort2"
-SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,/path/to/rundir,"patient1"
-SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,/path/to/rundir,"patient2"
-SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,/path/to/rundir,"patient3"
+SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz,/path/to/rundir,paired_sample:lane1
+SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A2_S2_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A2_S2_L002_R2_001.fastq.gz,/path/to/rundir,paired_sample:lane1
+SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A3_S3_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A3_S3_L002_R2_001.fastq.gz,/path/to/rundir,paired_sample:lane2
+SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,/path/to/rundir,group1
+SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,/path/to/rundir,group2
+SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,/path/to/rundir,group3
diff --git a/assets/schema_input.json b/assets/schema_input.json
index d4a6dc7..3569ae2 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -36,8 +36,8 @@
             },
             "tags": {
                 "type": "string",
-                "pattern": "^\\\"([A-Za-z0-9_-]+,\\ ?)*([A-Za-z0-9_-]+)\\\"$",
-                "errorMessage": "Tags must consist of numbers, letters, underscores or dashes and must be provided as a comma-separated list flanked by a pair of double-quotes, e.g. \"patient_01, lane1, pos-CTRL_2\".",
+                "pattern": "^([A-Za-z0-9_-]+:)*([A-Za-z0-9_-]+)$",
+                "errorMessage": "Tags must consist of numbers, letters, underscores or dashes and must be provided as a column-separated list, e.g. group_01:lane1:pos-CTRL_2.",
                 "meta": ["tags"]
             }
         },
diff --git a/docs/usage.md b/docs/usage.md
index 621c7c0..38a039c 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -32,10 +32,10 @@ run_dir
 
 ```csv title="samplesheet.csv"
 sample  fastq_1                                       fastq_2 rundir          tags
-sample1 path/to/run_dir/sample1_lane1_group1_r1.fq.gz         path/to/run_dir "project1,group1"
-sample2 path/to/run_dir/sample2_lane1_group1_r1.fq.gz         path/to/run_dir "project1,group1"
-sample3 path/to/run_dir/sample3_lane2_group2_r1.fq.gz         path/to/run_dir "project1,group2"
-sample4 path/to/run_dir/sample4_lane2_group3_r1.fq.gz         path/to/run_dir "control"
+sample1 path/to/run_dir/sample1_lane1_group1_r1.fq.gz         path/to/run_dir project1:group1
+sample2 path/to/run_dir/sample2_lane1_group1_r1.fq.gz         path/to/run_dir project1:group1
+sample3 path/to/run_dir/sample3_lane2_group2_r1.fq.gz         path/to/run_dir project1:group2
+sample4 path/to/run_dir/sample4_lane2_group3_r1.fq.gz         path/to/run_dir control
 
 ```
 
@@ -45,7 +45,7 @@ sample4 path/to/run_dir/sample4_lane2_group3_r1.fq.gz         path/to/run_dir "c
 | `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".                                                             |
 | `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz" (optional).                                                  |
 | `rundir`  | Path to the runfolder containing extra information about the sequencing run (optional) .                                                                                               |
-| `tags`    | Comma-separated list of tags to group samples in special reports.                                                                                                                      |
+| `tags`    | Column-separated list of tags to group samples in special reports.                                                                                                                     |
 
 Another [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.
 
diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index bb875af..eec4d09 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -84,7 +84,7 @@ workflow PIPELINE_INITIALISATION {
         .fromSamplesheet("input") // Validates samplesheet against $projectDir/assets/schema_input.json. Path to validation schema is defined by $projectDir/nextflow_schema.json
         .map {
             meta, fastq_1, fastq_2 ->
-                def tags = meta.tags ? meta.tags.tokenize(",") : []
+                def tags = meta.tags ? meta.tags.tokenize(":") : []
                 def updated_meta = meta + [ id:meta.sample, tags:tags ]
                 if (!fastq_2) {
                     return [ updated_meta.id, updated_meta + [ single_end:true ], [ fastq_1 ] ]
diff --git a/tests/NovaSeq6000.main.nf.test b/tests/NovaSeq6000.main.nf.test
index f93891b..d050399 100644
--- a/tests/NovaSeq6000.main.nf.test
+++ b/tests/NovaSeq6000.main.nf.test
@@ -23,20 +23,20 @@ nextflow_pipeline {
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_general_stats.txt"),
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_software_versions.txt"),
 
-                    path("$outputDir/multiqc/group_reports/cohort1/multiqc_data/multiqc_citations.txt"),
-                    path("$outputDir/multiqc/group_reports/cohort1/multiqc_data/multiqc_fastqc.txt"),
-                    path("$outputDir/multiqc/group_reports/cohort1/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/group_reports/cohort1/multiqc_data/multiqc_software_versions.txt"),
-
-                    path("$outputDir/multiqc/group_reports/patient1/multiqc_data/multiqc_citations.txt"),
-                    path("$outputDir/multiqc/group_reports/patient1/multiqc_data/multiqc_fastqc.txt"),
-                    path("$outputDir/multiqc/group_reports/patient1/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/group_reports/patient1/multiqc_data/multiqc_software_versions.txt"),
-
-                    path("$outputDir/multiqc/group_reports/patient2/multiqc_data/multiqc_citations.txt"),
-                    path("$outputDir/multiqc/group_reports/patient2/multiqc_data/multiqc_fastqc.txt"),
-                    path("$outputDir/multiqc/group_reports/patient2/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/group_reports/patient2/multiqc_data/multiqc_software_versions.txt"),
+                    path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_software_versions.txt"),
+
+                    path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_software_versions.txt"),
+
+                    path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_citations.txt"),
+                    path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_fastqc.txt"),
+                    path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_general_stats.txt"),
+                    path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_software_versions.txt"),
 
                     path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_fastqc.txt"),

From 8779909fe25a35950a999847d0b052b1f188de9c Mon Sep 17 00:00:00 2001
From: kedhammar <alfred.kedhammar@scilifelab.se>
Date: Tue, 3 Sep 2024 13:55:23 +0200
Subject: [PATCH 44/58] switch to colon-separated tags

---
 README.md                                            |  2 +-
 assets/samplesheet.csv                               | 12 ++++++------
 assets/schema_input.json                             |  4 ++--
 docs/usage.md                                        | 12 ++++++------
 .../local/utils_nfcore_seqinspector_pipeline/main.nf |  2 +-
 5 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/README.md b/README.md
index 31018e7..acba2ce 100644
--- a/README.md
+++ b/README.md
@@ -45,7 +45,7 @@ First, prepare a samplesheet with your input data that looks as follows:
 
 ```csv
 sample,fastq_1,fastq_2,rundir,tags
-CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,"patient1"
+CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,lane1:project5:group2
 ```
 
 Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv
index 00019e5..de5f1a6 100644
--- a/assets/samplesheet.csv
+++ b/assets/samplesheet.csv
@@ -1,7 +1,7 @@
 sample,fastq_1,fastq_2,rundir,tags
-SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz,/path/to/rundir,"paired_sample,cohort1"
-SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A2_S2_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A2_S2_L002_R2_001.fastq.gz,/path/to/rundir,"paired_sample,cohort1"
-SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A3_S3_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A3_S3_L002_R2_001.fastq.gz,/path/to/rundir,"paired_sample,cohort2"
-SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,/path/to/rundir,"patient1"
-SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,/path/to/rundir,"patient2"
-SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,/path/to/rundir,"patient3"
+SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz,/path/to/rundir,paired_sample:cohort1
+SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A2_S2_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A2_S2_L002_R2_001.fastq.gz,/path/to/rundir,paired_sample:cohort1
+SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A3_S3_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A3_S3_L002_R2_001.fastq.gz,/path/to/rundir,paired_sample:cohort2
+SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,/path/to/rundir,patient1
+SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,/path/to/rundir,patient2
+SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,/path/to/rundir,patient3
diff --git a/assets/schema_input.json b/assets/schema_input.json
index d4a6dc7..1894155 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -36,8 +36,8 @@
             },
             "tags": {
                 "type": "string",
-                "pattern": "^\\\"([A-Za-z0-9_-]+,\\ ?)*([A-Za-z0-9_-]+)\\\"$",
-                "errorMessage": "Tags must consist of numbers, letters, underscores or dashes and must be provided as a comma-separated list flanked by a pair of double-quotes, e.g. \"patient_01, lane1, pos-CTRL_2\".",
+                "pattern": "^([a-z0-9_-]+:)*([a-z0-9_-]+)$",
+                "errorMessage": "Tags must be separated by colons and only consist of lowercase letters, numbers, underscores and hyphens.",
                 "meta": ["tags"]
             }
         },
diff --git a/docs/usage.md b/docs/usage.md
index 42d596b..e2da41d 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -32,10 +32,10 @@ run_dir
 
 ```csv title="samplesheet.csv"
 sample  fastq_1                                       fastq_2 rundir          tags
-sample1 path/to/run_dir/sample1_lane1_group1_r1.fq.gz         path/to/run_dir "cohort1,patient1"
-sample2 path/to/run_dir/sample2_lane1_group1_r1.fq.gz         path/to/run_dir "cohort1,patient2"
-sample3 path/to/run_dir/sample3_lane2_group2_r1.fq.gz         path/to/run_dir "cohort1,patient3"
-sample4 path/to/run_dir/sample4_lane2_group3_r1.fq.gz         path/to/run_dir "control"
+sample1 path/to/run_dir/sample1_lane1_group1_r1.fq.gz         path/to/run_dir cohort1:patient1
+sample2 path/to/run_dir/sample2_lane1_group1_r1.fq.gz         path/to/run_dir cohort1:patient2
+sample3 path/to/run_dir/sample3_lane2_group2_r1.fq.gz         path/to/run_dir cohort1:patient3
+sample4 path/to/run_dir/sample4_lane2_group3_r1.fq.gz         path/to/run_dir control
 
 ```
 
@@ -44,8 +44,8 @@ sample4 path/to/run_dir/sample4_lane2_group3_r1.fq.gz         path/to/run_dir "c
 | `sample`  | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). |
 | `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".                                                             |
 | `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz" (optional).                                                  |
-| `rundir`  | Path to the runfolder containing extra information about the sequencing run (optional) .                                                                                               |
-| `tags`    | Comma-separated list of tags to group samples in special reports.                                                                                                                      |
+| `rundir`  | Path to the runfolder containing extra information about the sequencing run (optional).                                                                                               |
+| `tags`    | Colon-separated list of tags to group samples in special reports.                                                                                                                      |
 
 Another [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.
 
diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index afcfc68..0ebfdd0 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -84,7 +84,7 @@ workflow PIPELINE_INITIALISATION {
         .fromSamplesheet("input") // Validates samplesheet against $projectDir/assets/schema_input.json. Path to validation schema is defined by $projectDir/nextflow_schema.json
         .map {
             meta, fastq_1, fastq_2 ->
-                def tags = meta.tags ? meta.tags.tokenize(",") : []
+                def tags = meta.tags ? meta.tags.tokenize(":") : []
                 def updated_meta = meta + [ id:meta.sample, tags:tags ]
                 if (!fastq_2) {
                     return [ updated_meta.id, updated_meta + [ single_end:true ], [ fastq_1 ] ]

From f496b85d07540807a452a094fb9cbc52013cc9f1 Mon Sep 17 00:00:00 2001
From: kedhammar <alfred.kedhammar@scilifelab.se>
Date: Tue, 3 Sep 2024 13:55:30 +0200
Subject: [PATCH 45/58] use testdata with tags

---
 conf/test.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/test.config b/conf/test.config
index 658e75f..c458ad0 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -22,7 +22,7 @@ params {
     // Input data
     // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
-    input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/MiSeq/samplesheet.csv'
+    input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/NovaSeq6000/samplesheet.csv'
 
     // Genome references
     genome = 'R64-1-1'

From 38e39a9828646f984e7902bd119b802e288624c9 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Tue, 3 Sep 2024 14:10:16 +0200
Subject: [PATCH 46/58] Make ids unique

---
 .../local/utils_nfcore_seqinspector_pipeline/main.nf | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index eec4d09..632acb3 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -87,9 +87,17 @@ workflow PIPELINE_INITIALISATION {
                 def tags = meta.tags ? meta.tags.tokenize(":") : []
                 def updated_meta = meta + [ id:meta.sample, tags:tags ]
                 if (!fastq_2) {
-                    return [ updated_meta.id, updated_meta + [ single_end:true ], [ fastq_1 ] ]
+                    return [
+                        updated_meta.id + fastq_1.toString().replaceAll('/', '_'),
+                        updated_meta + [ single_end:true ],
+                        [ fastq_1 ]
+                    ]
                 } else {
-                    return [ updated_meta.id, updated_meta + [ single_end:false ], [ fastq_1, fastq_2 ] ]
+                    return [
+                        updated_meta.id + fastq_1.toString().replaceAll('/', '_') + '_' + fastq_2.toString().replaceAll('/', '_'),
+                        updated_meta + [ single_end:false ],
+                        [ fastq_1, fastq_2 ]
+                    ]
                 }
         }
         .groupTuple()

From c96a41c0c6f5c4d3b7f8ff0d71242fd876b04325 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Tue, 3 Sep 2024 12:26:11 +0000
Subject: [PATCH 47/58] bump multiqc to prevent gitpod crashing, populate the
 new process inputs w. empty channels

---
 modules.json                                  |  2 +-
 modules/nf-core/multiqc/environment.yml       |  2 +-
 modules/nf-core/multiqc/main.nf               | 14 ++++++++++---
 modules/nf-core/multiqc/meta.yml              | 13 ++++++++++++
 modules/nf-core/multiqc/tests/main.nf.test    |  8 ++++++++
 .../nf-core/multiqc/tests/main.nf.test.snap   | 20 +++++++++----------
 modules/nf-core/multiqc/tests/nextflow.config |  5 +++++
 workflows/seqinspector.nf                     |  8 ++++++--
 8 files changed, 55 insertions(+), 17 deletions(-)
 create mode 100644 modules/nf-core/multiqc/tests/nextflow.config

diff --git a/modules.json b/modules.json
index 87fe816..70f3486 100644
--- a/modules.json
+++ b/modules.json
@@ -12,7 +12,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
+                        "git_sha": "19ca321db5d8bd48923262c2eca6422359633491",
                         "installed_by": ["modules"]
                     }
                 }
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index ca39fb6..a31464c 100644
--- a/modules/nf-core/multiqc/environment.yml
+++ b/modules/nf-core/multiqc/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::multiqc=1.21
+  - bioconda::multiqc=1.24.1
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index 47ac352..ceaec13 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -3,14 +3,16 @@ process MULTIQC {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.21--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.24.1--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.24.1--pyhdfd78af_0' }"
 
     input:
     path  multiqc_files, stageAs: "?/*"
     path(multiqc_config)
     path(extra_multiqc_config)
     path(multiqc_logo)
+    path(replace_names)
+    path(sample_names)
 
     output:
     path "*multiqc_report.html", emit: report
@@ -23,16 +25,22 @@ process MULTIQC {
 
     script:
     def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ? "--filename ${task.ext.prefix}.html" : ''
     def config = multiqc_config ? "--config $multiqc_config" : ''
     def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : ''
-    def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : ''
+    def logo = multiqc_logo ? "--cl-config 'custom_logo: \"${multiqc_logo}\"'" : ''
+    def replace = replace_names ? "--replace-names ${replace_names}" : ''
+    def samples = sample_names ? "--sample-names ${sample_names}" : ''
     """
     multiqc \\
         --force \\
         $args \\
         $config \\
+        $prefix \\
         $extra_config \\
         $logo \\
+        $replace \\
+        $samples \\
         .
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
index 45a9bc3..382c08c 100644
--- a/modules/nf-core/multiqc/meta.yml
+++ b/modules/nf-core/multiqc/meta.yml
@@ -29,6 +29,19 @@ input:
       type: file
       description: Optional logo file for MultiQC
       pattern: "*.{png}"
+  - replace_names:
+      type: file
+      description: |
+        Optional two-column sample renaming file. First column a set of
+        patterns, second column a set of corresponding replacements. Passed via
+        MultiQC's `--replace-names` option.
+      pattern: "*.{tsv}"
+  - sample_names:
+      type: file
+      description: |
+        Optional TSV file with headers, passed to the MultiQC --sample_names
+        argument.
+      pattern: "*.{tsv}"
 output:
   - report:
       type: file
diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test
index f1c4242..33316a7 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test
+++ b/modules/nf-core/multiqc/tests/main.nf.test
@@ -8,6 +8,8 @@ nextflow_process {
     tag "modules_nfcore"
     tag "multiqc"
 
+    config "./nextflow.config"
+
     test("sarscov2 single-end [fastqc]") {
 
         when {
@@ -17,6 +19,8 @@ nextflow_process {
                 input[1] = []
                 input[2] = []
                 input[3] = []
+                input[4] = []
+                input[5] = []
                 """
             }
         }
@@ -41,6 +45,8 @@ nextflow_process {
                 input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true))
                 input[2] = []
                 input[3] = []
+                input[4] = []
+                input[5] = []
                 """
             }
         }
@@ -66,6 +72,8 @@ nextflow_process {
                 input[1] = []
                 input[2] = []
                 input[3] = []
+                input[4] = []
+                input[5] = []
                 """
             }
         }
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
index bfebd80..83fa080 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -2,14 +2,14 @@
     "multiqc_versions_single": {
         "content": [
             [
-                "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d"
+                "versions.yml:md5,6eb13f3b11bbcbfc98ad3166420ff760"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-02-29T08:48:55.657331"
+        "timestamp": "2024-07-10T12:41:34.562023"
     },
     "multiqc_stub": {
         "content": [
@@ -17,25 +17,25 @@
                 "multiqc_report.html",
                 "multiqc_data",
                 "multiqc_plots",
-                "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d"
+                "versions.yml:md5,6eb13f3b11bbcbfc98ad3166420ff760"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-02-29T08:49:49.071937"
+        "timestamp": "2024-07-10T11:27:11.933869532"
     },
     "multiqc_versions_config": {
         "content": [
             [
-                "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d"
+                "versions.yml:md5,6eb13f3b11bbcbfc98ad3166420ff760"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-02-29T08:49:25.457567"
+        "timestamp": "2024-07-10T11:26:56.709849369"
     }
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/multiqc/tests/nextflow.config b/modules/nf-core/multiqc/tests/nextflow.config
new file mode 100644
index 0000000..c537a6a
--- /dev/null
+++ b/modules/nf-core/multiqc/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: 'MULTIQC' {
+        ext.prefix = null
+    }
+}
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index e37df50..1ba00c6 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -89,7 +89,9 @@ workflow SEQINSPECTOR {
             .collect(),
         ch_multiqc_config.toList(),
         Channel.empty().toList(),
-        ch_multiqc_logo.toList()
+        ch_multiqc_logo.toList(),
+        Channel.empty().toList(),
+        Channel.empty().toList()
     )
 
     ch_tags = ch_multiqc_files
@@ -131,7 +133,9 @@ workflow SEQINSPECTOR {
         tagged_mqc_files.samples_per_tag,
         ch_multiqc_config.toList(),
         tagged_mqc_files.config,
-        ch_multiqc_logo.toList()
+        ch_multiqc_logo.toList(),
+        Channel.empty().toList(),
+        Channel.empty().toList()
     )
 
     emit:

From 2e269ecc236a66866f8413a1129656ed9c1d816f Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Tue, 3 Sep 2024 16:36:59 +0200
Subject: [PATCH 48/58] Allow for uppercase letters

---
 assets/schema_input.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/assets/schema_input.json b/assets/schema_input.json
index 1894155..f244083 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -36,7 +36,7 @@
             },
             "tags": {
                 "type": "string",
-                "pattern": "^([a-z0-9_-]+:)*([a-z0-9_-]+)$",
+                "pattern": "^([A-Za-z0-9_-]+:)*([A-Za-z0-9_-]+)$",
                 "errorMessage": "Tags must be separated by colons and only consist of lowercase letters, numbers, underscores and hyphens.",
                 "meta": ["tags"]
             }

From c97a597e8165081565d5acb1afdfd61e83f6309c Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Tue, 10 Sep 2024 08:54:03 +0200
Subject: [PATCH 49/58] Use samplesheet row in id

Co-authored-by: Matthias Zepper <MatthiasZepper@users.noreply.github.com>
---
 .../local/utils_nfcore_seqinspector_pipeline/main.nf   | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index 632acb3..3c63037 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -82,19 +82,21 @@ workflow PIPELINE_INITIALISATION {
     //
     Channel
         .fromSamplesheet("input") // Validates samplesheet against $projectDir/assets/schema_input.json. Path to validation schema is defined by $projectDir/nextflow_schema.json
+        .toList()
+        .flatMap { it.withIndex().collect {  entry, idx -> entry + "${idx+1}" } }
         .map {
-            meta, fastq_1, fastq_2 ->
+            meta, fastq_1, fastq_2, idx ->
                 def tags = meta.tags ? meta.tags.tokenize(":") : []
-                def updated_meta = meta + [ id:meta.sample, tags:tags ]
+                def updated_meta = meta + [ id:"${meta.sample}_${idx}", tags:tags ]
                 if (!fastq_2) {
                     return [
-                        updated_meta.id + fastq_1.toString().replaceAll('/', '_'),
+                        updated_meta.id,
                         updated_meta + [ single_end:true ],
                         [ fastq_1 ]
                     ]
                 } else {
                     return [
-                        updated_meta.id + fastq_1.toString().replaceAll('/', '_') + '_' + fastq_2.toString().replaceAll('/', '_'),
+                        updated_meta.id,
                         updated_meta + [ single_end:false ],
                         [ fastq_1, fastq_2 ]
                     ]

From 1f33928fdc2f9350fbb4ea86e253f5f7cc9b6670 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Tue, 10 Sep 2024 09:03:50 +0200
Subject: [PATCH 50/58] Update snapshots

---
 tests/MiSeq.main.nf.test.snap       | 12 ++++++----
 tests/NovaSeq6000.main.nf.test.snap | 36 ++++++++++++++++-------------
 tests/PromethION.main.nf.test.snap  | 12 ++++++----
 3 files changed, 36 insertions(+), 24 deletions(-)

diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index 26f0c2a..9dacaf8 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -2,10 +2,14 @@
     "MiSeq data test": {
         "content": [
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,e46e7baa8f57d4cf54d973925b5eadf9",
-            "multiqc_general_stats.txt:md5,a5e626a2e1a3c986092e4f89091cc41c",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95"
+            "multiqc_fastqc.txt:md5,7b1b7fd457b60404768045b148d4c0a8",
+            "multiqc_general_stats.txt:md5,962713a1473a318f2cb29bb5290c4c8e",
+            "multiqc_software_versions.txt:md5,49e3596d49ee49d967d3b6c363b486d5"
         ],
-        "timestamp": "2024-08-26T17:55:16.152573"
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-10T08:57:05.870194"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index f5c4776..3f27e5a 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -2,26 +2,30 @@
     "NovaSeq6000 data test": {
         "content": [
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,e8ed6dca928396b8873d24e60ea1a133",
-            "multiqc_general_stats.txt:md5,fd9d46c5b441908cd07e5373d116db17",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
+            "multiqc_fastqc.txt:md5,3730f9046b20ac5c17a86db0a33f8d5d",
+            "multiqc_general_stats.txt:md5,d521de54d1e659bf7892105f7d23d4db",
+            "multiqc_software_versions.txt:md5,49e3596d49ee49d967d3b6c363b486d5",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,ff9b31c6024f11a8135456e7ea01fc8f",
-            "multiqc_general_stats.txt:md5,f36bd6e27e92c25be076efea411d3a8e",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
+            "multiqc_fastqc.txt:md5,8284e25ccc21041cf3b5a32eb6a51e78",
+            "multiqc_general_stats.txt:md5,d52544eb1a505c889a2f9117cf94a5fa",
+            "multiqc_software_versions.txt:md5,49e3596d49ee49d967d3b6c363b486d5",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,62d51280dcd7634f6bed95ffe0d8dab8",
-            "multiqc_general_stats.txt:md5,2012002b6a057be981a97fcc96142a6c",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
+            "multiqc_fastqc.txt:md5,f38ffdc112c73af3a41ed15848a3761f",
+            "multiqc_general_stats.txt:md5,5b1190093085ef073d4bd5818c9cde79",
+            "multiqc_software_versions.txt:md5,49e3596d49ee49d967d3b6c363b486d5",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,63749e803a2d5fc7ecc7cd93fa68df1f",
-            "multiqc_general_stats.txt:md5,656931993032400dea3d441b8b61b4d2",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95",
+            "multiqc_fastqc.txt:md5,7ff71ceb8ecdf086331047f8860c3347",
+            "multiqc_general_stats.txt:md5,79c1090dd8a97912893f8491641b9dc9",
+            "multiqc_software_versions.txt:md5,49e3596d49ee49d967d3b6c363b486d5",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,91cc62e1b4059bdbe4b88affa43378af",
-            "multiqc_general_stats.txt:md5,6e500f82550e00b07c3e7aa1d46ab9e9",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95"
+            "multiqc_fastqc.txt:md5,519ff344a896ac369bba4d5c5b8be7b5",
+            "multiqc_general_stats.txt:md5,41611bd5ab9e79425c466bf976b03bdc",
+            "multiqc_software_versions.txt:md5,49e3596d49ee49d967d3b6c363b486d5"
         ],
-        "timestamp": "2024-08-26T18:03:33.089142"
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-10T08:58:26.732622"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index e3b34f2..fb8cda2 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -2,10 +2,14 @@
     "PromethION data test": {
         "content": [
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,cecee3cb343c75c80180d3169c6f3ea1",
-            "multiqc_general_stats.txt:md5,e63c25089c4fc10618414ba2254d18c7",
-            "multiqc_software_versions.txt:md5,7452f1f7aae2a8a4066c2ef6cd5ceb95"
+            "multiqc_fastqc.txt:md5,35984961f25a0d4e7352cab4d5650178",
+            "multiqc_general_stats.txt:md5,1465b0b1959e3864b28ecc2340df351b",
+            "multiqc_software_versions.txt:md5,49e3596d49ee49d967d3b6c363b486d5"
         ],
-        "timestamp": "2024-08-26T17:55:38.755385"
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-10T08:58:57.180636"
     }
 }
\ No newline at end of file

From f530e314af225eb3d5fa61fd31a59e3861bae1d6 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Tue, 8 Oct 2024 12:33:12 +0000
Subject: [PATCH 51/58] Template update for nf-core/tools version 3.0.0

---
 .editorconfig                                 |   4 +
 .github/CONTRIBUTING.md                       |  10 +-
 .github/PULL_REQUEST_TEMPLATE.md              |   2 +-
 .github/workflows/awsfulltest.yml             |  23 +-
 .github/workflows/ci.yml                      |  17 +-
 .github/workflows/download_pipeline.yml       |  53 ++-
 .github/workflows/linting.yml                 |  23 +-
 .github/workflows/linting_comment.yml         |   2 +-
 .github/workflows/release-announcements.yml   |   2 +-
 .../workflows/template_version_comment.yml    |  43 ++
 .gitpod.yml                                   |   7 +-
 .nf-core.yml                                  |  16 +-
 .pre-commit-config.yaml                       |   2 +-
 .prettierignore                               |   1 +
 CITATIONS.md                                  |   4 +-
 README.md                                     |   5 +-
 assets/schema_input.json                      |   2 +-
 conf/base.config                              |  34 +-
 conf/igenomes_ignored.config                  |   9 +
 conf/modules.config                           |   1 -
 conf/test.config                              |  13 +-
 docs/images/mqc_fastqc_adapter.png            | Bin 23458 -> 0 bytes
 docs/images/mqc_fastqc_counts.png             | Bin 33918 -> 0 bytes
 docs/images/mqc_fastqc_quality.png            | Bin 55769 -> 0 bytes
 docs/output.md                                |  11 +-
 docs/usage.md                                 |  12 +-
 main.nf                                       |  10 +-
 modules.json                                  |  12 +-
 modules/nf-core/fastqc/environment.yml        |   2 -
 modules/nf-core/fastqc/main.nf                |   5 +-
 modules/nf-core/fastqc/meta.yml               |  57 +--
 modules/nf-core/fastqc/tests/main.nf.test     | 225 ++++++++---
 .../nf-core/fastqc/tests/main.nf.test.snap    | 370 ++++++++++++++++--
 modules/nf-core/multiqc/environment.yml       |   4 +-
 modules/nf-core/multiqc/main.nf               |  14 +-
 modules/nf-core/multiqc/meta.yml              |  78 ++--
 modules/nf-core/multiqc/tests/main.nf.test    |   8 +
 .../nf-core/multiqc/tests/main.nf.test.snap   |  20 +-
 modules/nf-core/multiqc/tests/nextflow.config |   5 +
 nextflow.config                               | 146 ++++---
 nextflow_schema.json                          |  85 +---
 .../main.nf                                   |  56 +--
 .../nf-core/utils_nextflow_pipeline/main.nf   |  24 +-
 .../tests/nextflow.config                     |   2 +-
 .../nf-core/utils_nfcore_pipeline/main.nf     |  45 ++-
 .../nf-core/utils_nfschema_plugin/main.nf     |  46 +++
 .../nf-core/utils_nfschema_plugin/meta.yml    |  35 ++
 .../utils_nfschema_plugin/tests/main.nf.test  | 117 ++++++
 .../tests/nextflow.config                     |   8 +
 .../tests/nextflow_schema.json                |   8 +-
 .../nf-core/utils_nfvalidation_plugin/main.nf |  62 ---
 .../utils_nfvalidation_plugin/meta.yml        |  44 ---
 .../tests/main.nf.test                        | 200 ----------
 .../utils_nfvalidation_plugin/tests/tags.yml  |   2 -
 workflows/seqinspector.nf                     |  23 +-
 55 files changed, 1203 insertions(+), 806 deletions(-)
 create mode 100644 .github/workflows/template_version_comment.yml
 create mode 100644 conf/igenomes_ignored.config
 delete mode 100755 docs/images/mqc_fastqc_adapter.png
 delete mode 100755 docs/images/mqc_fastqc_counts.png
 delete mode 100755 docs/images/mqc_fastqc_quality.png
 create mode 100644 modules/nf-core/multiqc/tests/nextflow.config
 create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/main.nf
 create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/meta.yml
 create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
 create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
 rename subworkflows/nf-core/{utils_nfvalidation_plugin => utils_nfschema_plugin}/tests/nextflow_schema.json (95%)
 delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
 delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml
 delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
 delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml

diff --git a/.editorconfig b/.editorconfig
index 72dda28..e105881 100644
--- a/.editorconfig
+++ b/.editorconfig
@@ -11,6 +11,7 @@ indent_style = space
 [*.{md,yml,yaml,html,css,scss,js}]
 indent_size = 2
 
+
 # These files are edited and tested upstream in nf-core/modules
 [/modules/nf-core/**]
 charset = unset
@@ -25,9 +26,12 @@ insert_final_newline = unset
 trim_trailing_whitespace = unset
 indent_style = unset
 
+
+
 [/assets/email*]
 indent_size = unset
 
+
 # ignore python and markdown
 [*.{py,md}]
 indent_style = unset
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index ee3dfbd..78893ac 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -19,7 +19,7 @@ If you'd like to write some code for nf-core/seqinspector, the standard workflow
 1. Check that there isn't already an issue about your idea in the [nf-core/seqinspector issues](https://github.com/nf-core/seqinspector/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
 2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/seqinspector repository](https://github.com/nf-core/seqinspector) to your GitHub account
 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
-4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
+4. Use `nf-core pipelines schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
 5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
 
 If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/).
@@ -40,7 +40,7 @@ There are typically two types of tests that run:
 ### Lint tests
 
 `nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to.
-To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint <pipeline-directory>` command.
+To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core pipelines lint <pipeline-directory>` command.
 
 If any failures or warnings are encountered, please follow the listed URL for more documentation.
 
@@ -75,7 +75,7 @@ If you wish to contribute a new step, please use the following coding standards:
 2. Write the process block (see below).
 3. Define the output channel if needed (see below).
 4. Add any new parameters to `nextflow.config` with a default (see below).
-5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core schema build` tool).
+5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool).
 6. Add sanity checks and validation for all relevant parameters.
 7. Perform local tests to validate that the new code works as expected.
 8. If applicable, add a new test command in `.github/workflow/ci.yml`.
@@ -86,7 +86,7 @@ If you wish to contribute a new step, please use the following coding standards:
 
 Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope.
 
-Once there, use `nf-core schema build` to add to `nextflow_schema.json`.
+Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`.
 
 ### Default processes resource requirements
 
@@ -103,7 +103,7 @@ Please use the following naming schemes, to make it easy to understand what is g
 
 ### Nextflow version bumping
 
-If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core bump-version --nextflow . [min-nf-version]`
+If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core pipelines bump-version --nextflow . [min-nf-version]`
 
 ### Images and figures
 
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index 6de151f..9dcf6a3 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -17,7 +17,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/seqi
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
 - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/seqinspector/tree/master/.github/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/seqinspector _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
-- [ ] Make sure your code lints (`nf-core lint`).
+- [ ] Make sure your code lints (`nf-core pipelines lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index 9278410..c9462a5 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -1,18 +1,33 @@
 name: nf-core AWS full size tests
-# This workflow is triggered on published releases.
+# This workflow is triggered on PRs opened against the master branch.
 # It can be additionally triggered manually with GitHub actions workflow dispatch button.
 # It runs the -profile 'test_full' on AWS batch
 
 on:
-  release:
-    types: [published]
+  pull_request:
+    branches:
+      - master
   workflow_dispatch:
+  pull_request_review:
+    types: [submitted]
+
 jobs:
   run-platform:
     name: Run AWS full tests
-    if: github.repository == 'nf-core/seqinspector'
+    if: github.repository == 'nf-core/seqinspector' && github.event.review.state == 'approved'
     runs-on: ubuntu-latest
     steps:
+      - uses: octokit/request-action@v2.x
+        id: check_approvals
+        with:
+          route: GET /repos/${{ github.repository }}/pulls/${{ github.event.review.number }}/reviews
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - id: test_variables
+        run: |
+          JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'
+          CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length')
+          test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required
       - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
         # TODO nf-core: You can customise AWS full pipeline tests as required
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 59c9410..5666673 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -7,6 +7,7 @@ on:
   pull_request:
   release:
     types: [published]
+  workflow_dispatch:
 
 env:
   NXF_ANSI_LOG: false
@@ -24,7 +25,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "23.04.0"
+          - "24.04.2"
           - "latest-everything"
     steps:
       - name: Check out pipeline code
@@ -38,9 +39,21 @@ jobs:
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - name: Run pipeline with test data
+      - name: Run pipeline with test data (docker)
         # TODO nf-core: You can customise CI pipeline run tests as required
         # For example: adding multiple test runs with different parameters
         # Remember that you can parallelise this by using strategy.matrix
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
+
+      - name: Run pipeline with test data (singularity)
+        # TODO nf-core: You can customise CI pipeline run tests as required
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test,singularity --outdir ./results
+        if: "${{ github.base_ref == 'master' }}"
+
+      - name: Run pipeline with test data (conda)
+        # TODO nf-core: You can customise CI pipeline run tests as required
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test,conda --outdir ./results
+        if: "${{ github.base_ref == 'master' }}"
diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index 2d20d64..713dc3e 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -1,4 +1,4 @@
-name: Test successful pipeline download with 'nf-core download'
+name: Test successful pipeline download with 'nf-core pipelines download'
 
 # Run the workflow when:
 #  - dispatched manually
@@ -8,7 +8,7 @@ on:
   workflow_dispatch:
     inputs:
       testbranch:
-        description: "The specific branch you wish to utilize for the test execution of nf-core download."
+        description: "The specific branch you wish to utilize for the test execution of nf-core pipelines download."
         required: true
         default: "dev"
   pull_request:
@@ -39,9 +39,11 @@ jobs:
         with:
           python-version: "3.12"
           architecture: "x64"
-      - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7
+
+      - name: Setup Apptainer
+        uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0
         with:
-          singularity-version: 3.8.3
+          apptainer-version: 1.3.4
 
       - name: Install dependencies
         run: |
@@ -54,33 +56,64 @@ jobs:
           echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV}
           echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV}
 
+      - name: Make a cache directory for the container images
+        run: |
+          mkdir -p ./singularity_container_images
+
       - name: Download the pipeline
         env:
-          NXF_SINGULARITY_CACHEDIR: ./
+          NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
         run: |
-          nf-core download ${{ env.REPO_LOWERCASE }} \
+          nf-core pipelines download ${{ env.REPO_LOWERCASE }} \
           --revision ${{ env.REPO_BRANCH }} \
           --outdir ./${{ env.REPOTITLE_LOWERCASE }} \
           --compress "none" \
           --container-system 'singularity' \
-          --container-library "quay.io" -l "docker.io" -l "ghcr.io" \
+          --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io" \
           --container-cache-utilisation 'amend' \
-          --download-configuration
+          --download-configuration 'yes'
 
       - name: Inspect download
         run: tree ./${{ env.REPOTITLE_LOWERCASE }}
 
+      - name: Count the downloaded number of container images
+        id: count_initial
+        run: |
+          image_count=$(ls -1 ./singularity_container_images | wc -l | xargs)
+          echo "Initial container image count: $image_count"
+          echo "IMAGE_COUNT_INITIAL=$image_count" >> ${GITHUB_ENV}
+
       - name: Run the downloaded pipeline (stub)
         id: stub_run_pipeline
         continue-on-error: true
         env:
-          NXF_SINGULARITY_CACHEDIR: ./
+          NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
           NXF_SINGULARITY_HOME_MOUNT: true
         run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
       - name: Run the downloaded pipeline (stub run not supported)
         id: run_pipeline
         if: ${{ job.steps.stub_run_pipeline.status == failure() }}
         env:
-          NXF_SINGULARITY_CACHEDIR: ./
+          NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
           NXF_SINGULARITY_HOME_MOUNT: true
         run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results
+
+      - name: Count the downloaded number of container images
+        id: count_afterwards
+        run: |
+          image_count=$(ls -1 ./singularity_container_images | wc -l | xargs)
+          echo "Post-pipeline run container image count: $image_count"
+          echo "IMAGE_COUNT_AFTER=$image_count" >> ${GITHUB_ENV}
+
+      - name: Compare container image counts
+        run: |
+          if [ "${{ env.IMAGE_COUNT_INITIAL }}" -ne "${{ env.IMAGE_COUNT_AFTER }}" ]; then
+            initial_count=${{ env.IMAGE_COUNT_INITIAL }}
+            final_count=${{ env.IMAGE_COUNT_AFTER }}
+            difference=$((final_count - initial_count))
+            echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!"
+            tree ./singularity_container_images
+            exit 1
+          else
+            echo "The pipeline can be downloaded successfully!"
+          fi
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 1fcafe8..b882838 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -1,6 +1,6 @@
 name: nf-core linting
 # This workflow is triggered on pushes and PRs to the repository.
-# It runs the `nf-core lint` and markdown lint tests to ensure
+# It runs the `nf-core pipelines lint` and markdown lint tests to ensure
 # that the code meets the nf-core guidelines.
 on:
   push:
@@ -41,17 +41,32 @@ jobs:
           python-version: "3.12"
           architecture: "x64"
 
+      - name: read .nf-core.yml
+        uses: pietrobolcato/action-read-yaml@1.0.0
+        id: read_yml
+        with:
+          config: ${{ github.workspace }}/.nf-core.yaml
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install nf-core
+          pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
+
+      - name: Run nf-core pipelines lint
+        if: ${{ github.base_ref != 'master' }}
+        env:
+          GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
+        run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
 
-      - name: Run nf-core lint
+      - name: Run nf-core pipelines lint --release
+        if: ${{ github.base_ref == 'master' }}
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
-        run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
+        run: nf-core -l lint_log.txt pipelines lint --release --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
 
       - name: Save PR number
         if: ${{ always() }}
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index 40acc23..42e519b 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3
+        uses: dawidd6/action-download-artifact@bf251b5aa9c2f7eeb574a96ee720e24f801b7c11 # v6
         with:
           workflow: linting.yml
           workflow_conclusion: completed
diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
index 03ecfcf..c6ba35d 100644
--- a/.github/workflows/release-announcements.yml
+++ b/.github/workflows/release-announcements.yml
@@ -12,7 +12,7 @@ jobs:
       - name: get topics and convert to hashtags
         id: get_topics
         run: |
-          echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')"  >> $GITHUB_OUTPUT
+          echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" | sed 's/-//g' >> $GITHUB_OUTPUT
 
       - uses: rzr/fediverse-action@master
         with:
diff --git a/.github/workflows/template_version_comment.yml b/.github/workflows/template_version_comment.yml
new file mode 100644
index 0000000..9dea41f
--- /dev/null
+++ b/.github/workflows/template_version_comment.yml
@@ -0,0 +1,43 @@
+name: nf-core template version comment
+# This workflow is triggered on PRs to check if the pipeline template version matches the latest nf-core version.
+# It posts a comment to the PR, even if it comes from a fork.
+
+on: pull_request_target
+
+jobs:
+  template_version:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+
+      - name: Read template version from .nf-core.yml
+        uses: pietrobolcato/action-read-yaml@1.0.0
+        id: read_yml
+        with:
+          config: ${{ github.workspace }}/.nf-core.yml
+
+      - name: Install nf-core
+        run: |
+          python -m pip install --upgrade pip
+          pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
+
+      - name: Check nf-core outdated
+        id: nf_core_outdated
+        run: pip list --outdated | grep nf-core
+
+      - name: Post nf-core template version comment
+        uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
+        if: |
+          ${{ steps.nf_core_outdated.outputs.stdout }} =~ 'nf-core'
+        with:
+          repo-token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }}
+          allow-repeats: false
+          message: |
+            ## :warning: Newer version of the nf-core template is available.
+
+            Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}.
+            Please update your pipeline to the latest version.
+
+            For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync).
+          #
diff --git a/.gitpod.yml b/.gitpod.yml
index 105a182..4611863 100644
--- a/.gitpod.yml
+++ b/.gitpod.yml
@@ -4,17 +4,14 @@ tasks:
     command: |
       pre-commit install --install-hooks
       nextflow self-update
-  - name: unset JAVA_TOOL_OPTIONS
-    command: |
-      unset JAVA_TOOL_OPTIONS
 
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack
-    - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
+    #- esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
     - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
     - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
     - mechatroner.rainbow-csv # Highlight columns in csv files in different colors
-    # - nextflow.nextflow                    # Nextflow syntax highlighting
+    - nextflow.nextflow # Nextflow syntax highlighting
     - oderwat.indent-rainbow # Highlight indentation level
     - streetsidesoftware.code-spell-checker # Spelling checker for source code
     - charliermarsh.ruff # Code linter Ruff
diff --git a/.nf-core.yml b/.nf-core.yml
index e0b85a7..ca26523 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,2 +1,16 @@
+bump_version: null
+lint: null
+nf_core_version: 3.0.0
+org_path: null
 repository_type: pipeline
-nf_core_version: "2.14.1"
+template:
+  author: Adrien Coulier
+  description: Pipeline to QC your sequences
+  force: false
+  is_nfcore: true
+  name: seqinspector
+  org: nf-core
+  outdir: .
+  skip_features: null
+  version: 1.0dev
+update: null
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 4dc0f1d..9e9f0e1 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -7,7 +7,7 @@ repos:
           - prettier@3.2.5
 
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
-    rev: "2.7.3"
+    rev: "3.0.3"
     hooks:
       - id: editorconfig-checker
         alias: ec
diff --git a/.prettierignore b/.prettierignore
index 437d763..610e506 100644
--- a/.prettierignore
+++ b/.prettierignore
@@ -1,3 +1,4 @@
+
 email_template.html
 adaptivecard.json
 slackreport.json
diff --git a/CITATIONS.md b/CITATIONS.md
index a585425..ecbfb16 100644
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -12,11 +12,11 @@
 
 - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
-  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
+> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
 
 - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 
-  > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
+> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
 
 ## Software packaging/containerisation tools
 
diff --git a/README.md b/README.md
index bfb53fe..2b5e2c8 100644
--- a/README.md
+++ b/README.md
@@ -9,7 +9,7 @@
 [![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
@@ -67,8 +67,7 @@ nextflow run nf-core/seqinspector \
 ```
 
 > [!WARNING]
-> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
-> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
+> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).
 
 For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).
 
diff --git a/assets/schema_input.json b/assets/schema_input.json
index 338d355..d7d4837 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -1,5 +1,5 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "$id": "https://raw.githubusercontent.com/nf-core/seqinspector/master/assets/schema_input.json",
     "title": "nf-core/seqinspector pipeline - params.input schema",
     "description": "Schema for the file provided with params.input",
diff --git a/conf/base.config b/conf/base.config
index aab50f9..b8e828d 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -11,9 +11,9 @@
 process {
 
     // TODO nf-core: Check the defaults for all processes
-    cpus   = { check_max( 1    * task.attempt, 'cpus'   ) }
-    memory = { check_max( 6.GB * task.attempt, 'memory' ) }
-    time   = { check_max( 4.h  * task.attempt, 'time'   ) }
+    cpus   = { 1      * task.attempt }
+    memory = { 6.GB   * task.attempt }
+    time   = { 4.h    * task.attempt }
 
     errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
     maxRetries    = 1
@@ -27,30 +27,30 @@ process {
     // TODO nf-core: Customise requirements for specific processes.
     // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
     withLabel:process_single {
-        cpus   = { check_max( 1                  , 'cpus'    ) }
-        memory = { check_max( 6.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h  * task.attempt, 'time'    ) }
+        cpus   = { 1                   }
+        memory = { 6.GB * task.attempt }
+        time   = { 4.h  * task.attempt }
     }
     withLabel:process_low {
-        cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 12.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
+        cpus   = { 2     * task.attempt }
+        memory = { 12.GB * task.attempt }
+        time   = { 4.h   * task.attempt }
     }
     withLabel:process_medium {
-        cpus   = { check_max( 6     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 36.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 8.h   * task.attempt, 'time'    ) }
+        cpus   = { 6     * task.attempt }
+        memory = { 36.GB * task.attempt }
+        time   = { 8.h   * task.attempt }
     }
     withLabel:process_high {
-        cpus   = { check_max( 12    * task.attempt, 'cpus'    ) }
-        memory = { check_max( 72.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 16.h  * task.attempt, 'time'    ) }
+        cpus   = { 12    * task.attempt }
+        memory = { 72.GB * task.attempt }
+        time   = { 16.h  * task.attempt }
     }
     withLabel:process_long {
-        time   = { check_max( 20.h  * task.attempt, 'time'    ) }
+        time   = { 20.h  * task.attempt }
     }
     withLabel:process_high_memory {
-        memory = { check_max( 200.GB * task.attempt, 'memory' ) }
+        memory = { 200.GB * task.attempt }
     }
     withLabel:error_ignore {
         errorStrategy = 'ignore'
diff --git a/conf/igenomes_ignored.config b/conf/igenomes_ignored.config
new file mode 100644
index 0000000..b4034d8
--- /dev/null
+++ b/conf/igenomes_ignored.config
@@ -0,0 +1,9 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for iGenomes paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Empty genomes dictionary to use when igenomes is ignored.
+----------------------------------------------------------------------------------------
+*/
+
+params.genomes = [:]
diff --git a/conf/modules.config b/conf/modules.config
index d203d2b..d266a38 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -21,7 +21,6 @@ process {
     withName: FASTQC {
         ext.args = '--quiet'
     }
-
     withName: 'MULTIQC' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [
diff --git a/conf/test.config b/conf/test.config
index 6a7b984..1838ae5 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -10,15 +10,18 @@
 ----------------------------------------------------------------------------------------
 */
 
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '1.h'
+    ]
+}
+
 params {
     config_profile_name        = 'Test profile'
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
-
     // Input data
     // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
diff --git a/docs/images/mqc_fastqc_adapter.png b/docs/images/mqc_fastqc_adapter.png
deleted file mode 100755
index 361d0e47acfb424dea1f326590d1eb2f6dfa26b5..0000000000000000000000000000000000000000
GIT binary patch
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diff --git a/docs/output.md b/docs/output.md
index 77e4cc1..9184bd0 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -14,6 +14,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 - [FastQC](#fastqc) - Raw read QC
 - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
+
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
 ### FastQC
@@ -29,16 +30,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).
 
-![MultiQC - FastQC sequence counts plot](images/mqc_fastqc_counts.png)
-
-![MultiQC - FastQC mean quality scores plot](images/mqc_fastqc_quality.png)
-
-![MultiQC - FastQC adapter content plot](images/mqc_fastqc_adapter.png)
-
-:::note
-The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality.
-:::
-
 ### MultiQC
 
 <details markdown="1">
diff --git a/docs/usage.md b/docs/usage.md
index ec180e4..bbc141e 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -85,9 +85,9 @@ The above pipeline run specified with a params file in yaml format:
 nextflow run nf-core/seqinspector -profile docker -params-file params.yaml
 ```
 
-with `params.yaml` containing:
+with:
 
-```yaml
+```yaml title="params.yaml"
 input: './samplesheet.csv'
 outdir: './results/'
 genome: 'GRCh37'
@@ -199,14 +199,6 @@ See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config
 
 If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack) on the [`#configs` channel](https://nfcore.slack.com/channels/configs).
 
-## Azure Resource Requests
-
-To be used with the `azurebatch` profile by specifying the `-profile azurebatch`.
-We recommend providing a compute `params.vm_type` of `Standard_D16_v3` VMs by default but these options can be changed if required.
-
-Note that the choice of VM size depends on your quota and the overall workload during the analysis.
-For a thorough list, please refer the [Azure Sizes for virtual machines in Azure](https://docs.microsoft.com/en-us/azure/virtual-machines/sizes).
-
 ## Running in the background
 
 Nextflow handles job submissions and supervises the running jobs. The Nextflow process must run until the pipeline is finished.
diff --git a/main.nf b/main.nf
index 2e9b1e3..df5d216 100644
--- a/main.nf
+++ b/main.nf
@@ -9,8 +9,6 @@
 ----------------------------------------------------------------------------------------
 */
 
-nextflow.enable.dsl = 2
-
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
@@ -20,7 +18,6 @@ nextflow.enable.dsl = 2
 include { SEQINSPECTOR  } from './workflows/seqinspector'
 include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_seqinspector_pipeline'
 include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_seqinspector_pipeline'
-
 include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_seqinspector_pipeline'
 
 /*
@@ -56,10 +53,8 @@ workflow NFCORE_SEQINSPECTOR {
     SEQINSPECTOR (
         samplesheet
     )
-
     emit:
     multiqc_report = SEQINSPECTOR.out.multiqc_report // channel: /path/to/multiqc_report.html
-
 }
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -70,27 +65,24 @@ workflow NFCORE_SEQINSPECTOR {
 workflow {
 
     main:
-
     //
     // SUBWORKFLOW: Run initialisation tasks
     //
     PIPELINE_INITIALISATION (
         params.version,
-        params.help,
         params.validate_params,
         params.monochrome_logs,
         args,
         params.outdir,
         params.input
     )
-
+    
     //
     // WORKFLOW: Run main workflow
     //
     NFCORE_SEQINSPECTOR (
         PIPELINE_INITIALISATION.out.samplesheet
     )
-
     //
     // SUBWORKFLOW: Run completion tasks
     //
diff --git a/modules.json b/modules.json
index 87fe816..0ab8a79 100644
--- a/modules.json
+++ b/modules.json
@@ -7,12 +7,12 @@
                 "nf-core": {
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     }
                 }
@@ -21,17 +21,17 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
+                        "git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab",
                         "installed_by": ["subworkflows"]
                     },
-                    "utils_nfvalidation_plugin": {
+                    "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml
index 1787b38..691d4c7 100644
--- a/modules/nf-core/fastqc/environment.yml
+++ b/modules/nf-core/fastqc/environment.yml
@@ -1,7 +1,5 @@
-name: fastqc
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::fastqc=0.12.1
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index d79f1c8..d8989f4 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -26,7 +26,10 @@ process FASTQC {
     def rename_to = old_new_pairs*.join(' ').join(' ')
     def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
 
-    def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB')
+    // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory)
+    // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222
+    // Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label
+    def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') / task.cpus
     // FastQC memory value allowed range (100 - 10000)
     def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb)
 
diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml
index ee5507e..4827da7 100644
--- a/modules/nf-core/fastqc/meta.yml
+++ b/modules/nf-core/fastqc/meta.yml
@@ -16,35 +16,44 @@ tools:
       homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
       documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
       licence: ["GPL-2.0-only"]
+      identifier: biotools:fastqc
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - reads:
-      type: file
-      description: |
-        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
-        respectively.
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - reads:
+        type: file
+        description: |
+          List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+          respectively.
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
   - html:
-      type: file
-      description: FastQC report
-      pattern: "*_{fastqc.html}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.html":
+          type: file
+          description: FastQC report
+          pattern: "*_{fastqc.html}"
   - zip:
-      type: file
-      description: FastQC report archive
-      pattern: "*_{fastqc.zip}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.zip":
+          type: file
+          description: FastQC report archive
+          pattern: "*_{fastqc.zip}"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@drpatelh"
   - "@grst"
diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test
index 70edae4..e9d79a0 100644
--- a/modules/nf-core/fastqc/tests/main.nf.test
+++ b/modules/nf-core/fastqc/tests/main.nf.test
@@ -23,17 +23,14 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-
-            // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it.
-            // looks like this: <div id="header_filename">Mon 2 Oct 2023<br/>test.gz</div>
-            // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039
-
-            { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
-            { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
-            { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-
-            { assert snapshot(process.out.versions).match("fastqc_versions_single") }
+                { assert process.success },
+                // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it.
+                // looks like this: <div id="header_filename">Mon 2 Oct 2023<br/>test.gz</div>
+                // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039
+                { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
+                { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
+                { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert snapshot(process.out.versions).match() }
             )
         }
     }
@@ -54,16 +51,14 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-
-            { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
-            { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
-            { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
-            { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
-            { assert path(process.out.html[0][1][0]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-            { assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-
-            { assert snapshot(process.out.versions).match("fastqc_versions_paired") }
+                { assert process.success },
+                { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
+                { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
+                { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
+                { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
+                { assert path(process.out.html[0][1][0]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert snapshot(process.out.versions).match() }
             )
         }
     }
@@ -83,13 +78,11 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-
-            { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
-            { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
-            { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-
-            { assert snapshot(process.out.versions).match("fastqc_versions_interleaved") }
+                { assert process.success },
+                { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
+                { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
+                { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert snapshot(process.out.versions).match() }
             )
         }
     }
@@ -109,13 +102,11 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-
-            { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
-            { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
-            { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-
-            { assert snapshot(process.out.versions).match("fastqc_versions_bam") }
+                { assert process.success },
+                { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
+                { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
+                { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert snapshot(process.out.versions).match() }
             )
         }
     }
@@ -138,22 +129,20 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-
-            { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
-            { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
-            { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" },
-            { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" },
-            { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
-            { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
-            { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" },
-            { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" },
-            { assert path(process.out.html[0][1][0]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-            { assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-            { assert path(process.out.html[0][1][2]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-            { assert path(process.out.html[0][1][3]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-
-            { assert snapshot(process.out.versions).match("fastqc_versions_multiple") }
+                { assert process.success },
+                { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
+                { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
+                { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" },
+                { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" },
+                { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
+                { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
+                { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" },
+                { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" },
+                { assert path(process.out.html[0][1][0]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert path(process.out.html[0][1][2]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert path(process.out.html[0][1][3]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert snapshot(process.out.versions).match() }
             )
         }
     }
@@ -173,21 +162,18 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-
-            { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" },
-            { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" },
-            { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-
-            { assert snapshot(process.out.versions).match("fastqc_versions_custom_prefix") }
+                { assert process.success },
+                { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" },
+                { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" },
+                { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert snapshot(process.out.versions).match() }
             )
         }
     }
 
     test("sarscov2 single-end [fastq] - stub") {
 
-        options "-stub"
-
+    options "-stub"
         when {
             process {
                 """
@@ -201,12 +187,123 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-            { assert snapshot(process.out.html.collect { file(it[1]).getName() } +
-                                process.out.zip.collect { file(it[1]).getName() } +
-                                process.out.versions ).match("fastqc_stub") }
+                { assert process.success },
+                { assert snapshot(process.out).match() }
             )
         }
     }
 
+    test("sarscov2 paired-end [fastq] - stub") {
+
+    options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 interleaved [fastq] - stub") {
+
+    options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true)
+                ])
+            """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 paired-end [bam] - stub") {
+
+    options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 multiple [fastq] - stub") {
+
+    options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 custom_prefix - stub") {
+
+    options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'mysample', single_end:true ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
 }
diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap
index 86f7c31..d5db309 100644
--- a/modules/nf-core/fastqc/tests/main.nf.test.snap
+++ b/modules/nf-core/fastqc/tests/main.nf.test.snap
@@ -1,88 +1,392 @@
 {
-    "fastqc_versions_interleaved": {
+    "sarscov2 custom_prefix": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:40:07.293713"
+        "timestamp": "2024-07-22T11:02:16.374038"
     },
-    "fastqc_stub": {
+    "sarscov2 single-end [fastq] - stub": {
         "content": [
-            [
-                "test.html",
-                "test.zip",
-                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
-            ]
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:02:24.993809"
+    },
+    "sarscov2 custom_prefix - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "mysample",
+                            "single_end": true
+                        },
+                        "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "mysample",
+                            "single_end": true
+                        },
+                        "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "mysample",
+                            "single_end": true
+                        },
+                        "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "mysample",
+                            "single_end": true
+                        },
+                        "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:31:01.425198"
+        "timestamp": "2024-07-22T11:03:10.93942"
     },
-    "fastqc_versions_multiple": {
+    "sarscov2 interleaved [fastq]": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:40:55.797907"
+        "timestamp": "2024-07-22T11:01:42.355718"
     },
-    "fastqc_versions_bam": {
+    "sarscov2 paired-end [bam]": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:40:26.795862"
+        "timestamp": "2024-07-22T11:01:53.276274"
     },
-    "fastqc_versions_single": {
+    "sarscov2 multiple [fastq]": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:39:27.043675"
+        "timestamp": "2024-07-22T11:02:05.527626"
     },
-    "fastqc_versions_paired": {
+    "sarscov2 paired-end [fastq]": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:01:31.188871"
+    },
+    "sarscov2 paired-end [fastq] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:02:34.273566"
+    },
+    "sarscov2 multiple [fastq] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:39:47.584191"
+        "timestamp": "2024-07-22T11:03:02.304411"
     },
-    "fastqc_versions_custom_prefix": {
+    "sarscov2 single-end [fastq]": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:01:19.095607"
+    },
+    "sarscov2 interleaved [fastq] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:02:44.640184"
+    },
+    "sarscov2 paired-end [bam] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:41:14.576531"
+        "timestamp": "2024-07-22T11:02:53.550742"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index ca39fb6..f1cd99b 100644
--- a/modules/nf-core/multiqc/environment.yml
+++ b/modules/nf-core/multiqc/environment.yml
@@ -1,7 +1,5 @@
-name: multiqc
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - bioconda::multiqc=1.21
+  - bioconda::multiqc=1.24.1
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index 47ac352..b9ccebd 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -3,14 +3,16 @@ process MULTIQC {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.21--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.25--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.25--pyhdfd78af_0' }"
 
     input:
     path  multiqc_files, stageAs: "?/*"
     path(multiqc_config)
     path(extra_multiqc_config)
     path(multiqc_logo)
+    path(replace_names)
+    path(sample_names)
 
     output:
     path "*multiqc_report.html", emit: report
@@ -23,16 +25,22 @@ process MULTIQC {
 
     script:
     def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ? "--filename ${task.ext.prefix}.html" : ''
     def config = multiqc_config ? "--config $multiqc_config" : ''
     def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : ''
-    def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : ''
+    def logo = multiqc_logo ? "--cl-config 'custom_logo: \"${multiqc_logo}\"'" : ''
+    def replace = replace_names ? "--replace-names ${replace_names}" : ''
+    def samples = sample_names ? "--sample-names ${sample_names}" : ''
     """
     multiqc \\
         --force \\
         $args \\
         $config \\
+        $prefix \\
         $extra_config \\
         $logo \\
+        $replace \\
+        $samples \\
         .
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
index 45a9bc3..b16c187 100644
--- a/modules/nf-core/multiqc/meta.yml
+++ b/modules/nf-core/multiqc/meta.yml
@@ -1,5 +1,6 @@
 name: multiqc
-description: Aggregate results from bioinformatics analyses across many samples into a single report
+description: Aggregate results from bioinformatics analyses across many samples into
+  a single report
 keywords:
   - QC
   - bioinformatics tools
@@ -12,40 +13,59 @@ tools:
       homepage: https://multiqc.info/
       documentation: https://multiqc.info/docs/
       licence: ["GPL-3.0-or-later"]
+      identifier: biotools:multiqc
 input:
-  - multiqc_files:
-      type: file
-      description: |
-        List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
-  - multiqc_config:
-      type: file
-      description: Optional config yml for MultiQC
-      pattern: "*.{yml,yaml}"
-  - extra_multiqc_config:
-      type: file
-      description: Second optional config yml for MultiQC. Will override common sections in multiqc_config.
-      pattern: "*.{yml,yaml}"
-  - multiqc_logo:
-      type: file
-      description: Optional logo file for MultiQC
-      pattern: "*.{png}"
+  - - multiqc_files:
+        type: file
+        description: |
+          List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
+  - - multiqc_config:
+        type: file
+        description: Optional config yml for MultiQC
+        pattern: "*.{yml,yaml}"
+  - - extra_multiqc_config:
+        type: file
+        description: Second optional config yml for MultiQC. Will override common sections
+          in multiqc_config.
+        pattern: "*.{yml,yaml}"
+  - - multiqc_logo:
+        type: file
+        description: Optional logo file for MultiQC
+        pattern: "*.{png}"
+  - - replace_names:
+        type: file
+        description: |
+          Optional two-column sample renaming file. First column a set of
+          patterns, second column a set of corresponding replacements. Passed via
+          MultiQC's `--replace-names` option.
+        pattern: "*.{tsv}"
+  - - sample_names:
+        type: file
+        description: |
+          Optional TSV file with headers, passed to the MultiQC --sample_names
+          argument.
+        pattern: "*.{tsv}"
 output:
   - report:
-      type: file
-      description: MultiQC report file
-      pattern: "multiqc_report.html"
+      - "*multiqc_report.html":
+          type: file
+          description: MultiQC report file
+          pattern: "multiqc_report.html"
   - data:
-      type: directory
-      description: MultiQC data dir
-      pattern: "multiqc_data"
+      - "*_data":
+          type: directory
+          description: MultiQC data dir
+          pattern: "multiqc_data"
   - plots:
-      type: file
-      description: Plots created by MultiQC
-      pattern: "*_data"
+      - "*_plots":
+          type: file
+          description: Plots created by MultiQC
+          pattern: "*_data"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@abhi18av"
   - "@bunop"
diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test
index f1c4242..33316a7 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test
+++ b/modules/nf-core/multiqc/tests/main.nf.test
@@ -8,6 +8,8 @@ nextflow_process {
     tag "modules_nfcore"
     tag "multiqc"
 
+    config "./nextflow.config"
+
     test("sarscov2 single-end [fastqc]") {
 
         when {
@@ -17,6 +19,8 @@ nextflow_process {
                 input[1] = []
                 input[2] = []
                 input[3] = []
+                input[4] = []
+                input[5] = []
                 """
             }
         }
@@ -41,6 +45,8 @@ nextflow_process {
                 input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true))
                 input[2] = []
                 input[3] = []
+                input[4] = []
+                input[5] = []
                 """
             }
         }
@@ -66,6 +72,8 @@ nextflow_process {
                 input[1] = []
                 input[2] = []
                 input[3] = []
+                input[4] = []
+                input[5] = []
                 """
             }
         }
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
index bfebd80..b779e46 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -2,14 +2,14 @@
     "multiqc_versions_single": {
         "content": [
             [
-                "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d"
+                "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-02-29T08:48:55.657331"
+        "timestamp": "2024-07-10T12:41:34.562023"
     },
     "multiqc_stub": {
         "content": [
@@ -17,25 +17,25 @@
                 "multiqc_report.html",
                 "multiqc_data",
                 "multiqc_plots",
-                "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d"
+                "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-02-29T08:49:49.071937"
+        "timestamp": "2024-07-10T11:27:11.933869532"
     },
     "multiqc_versions_config": {
         "content": [
             [
-                "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d"
+                "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-02-29T08:49:25.457567"
+        "timestamp": "2024-07-10T11:26:56.709849369"
     }
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/multiqc/tests/nextflow.config b/modules/nf-core/multiqc/tests/nextflow.config
new file mode 100644
index 0000000..c537a6a
--- /dev/null
+++ b/modules/nf-core/multiqc/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: 'MULTIQC' {
+        ext.prefix = null
+    }
+}
diff --git a/nextflow.config b/nextflow.config
index a73f66b..90df166 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -16,7 +16,6 @@ params {
     genome                     = null
     igenomes_base              = 's3://ngi-igenomes/igenomes/'
     igenomes_ignore            = false
-
     // MultiQC options
     multiqc_config             = null
     multiqc_title              = null
@@ -33,48 +32,26 @@ params {
     monochrome_logs              = false
     hook_url                     = null
     help                         = false
+    help_full                    = false
+    show_hidden                  = false
     version                      = false
     pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
-
     // Config options
     config_profile_name        = null
     config_profile_description = null
+
     custom_config_version      = 'master'
     custom_config_base         = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
     config_profile_contact     = null
     config_profile_url         = null
-
-    // Max resource options
-    // Defaults only, expecting to be overwritten
-    max_memory                 = '128.GB'
-    max_cpus                   = 16
-    max_time                   = '240.h'
-
     // Schema validation default options
-    validationFailUnrecognisedParams = false
-    validationLenientMode            = false
-    validationSchemaIgnoreParams     = 'genomes,igenomes_base'
-    validationShowHiddenParams       = false
-    validate_params                  = true
-
+    validate_params            = true
+    
 }
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
 
-// Load nf-core custom profiles from different Institutions
-try {
-    includeConfig "${params.custom_config_base}/nfcore_custom.config"
-} catch (Exception e) {
-    System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
-}
-
-// Load nf-core/seqinspector custom profiles from different institutions.
-try {
-    includeConfig "${params.custom_config_base}/pipeline/seqinspector.config"
-} catch (Exception e) {
-    System.err.println("WARNING: Could not load nf-core/config/seqinspector profiles: ${params.custom_config_base}/pipeline/seqinspector.config")
-}
 profiles {
     debug {
         dumpHashes              = true
@@ -89,7 +66,7 @@ profiles {
         podman.enabled          = false
         shifter.enabled         = false
         charliecloud.enabled    = false
-        conda.channels          = ['conda-forge', 'bioconda', 'defaults']
+        conda.channels          = ['conda-forge', 'bioconda']
         apptainer.enabled       = false
     }
     mamba {
@@ -178,25 +155,23 @@ profiles {
     test_full { includeConfig 'conf/test_full.config' }
 }
 
-// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile
-// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled
-// Set to your registry if you have a mirror of containers
-apptainer.registry   = 'quay.io'
-docker.registry      = 'quay.io'
-podman.registry      = 'quay.io'
-singularity.registry = 'quay.io'
+// Load nf-core custom profiles from different Institutions
+includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
 
-// Nextflow plugins
-plugins {
-    id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet
-}
+// Load nf-core/seqinspector custom profiles from different institutions.
+// TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
+// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/seqinspector.config" : "/dev/null"
+// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
+// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
+// Set to your registry if you have a mirror of containers
+apptainer.registry    = 'quay.io'
+docker.registry       = 'quay.io'
+podman.registry       = 'quay.io'
+singularity.registry  = 'quay.io'
+charliecloud.registry = 'quay.io'
 
 // Load igenomes.config if required
-if (!params.igenomes_ignore) {
-    includeConfig 'conf/igenomes.config'
-} else {
-    params.genomes = [:]
-}
+includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config'
 // Export these variables to prevent local Python/R libraries from conflicting with those in the container
 // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
 // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
@@ -208,8 +183,15 @@ env {
     JULIA_DEPOT_PATH = "/usr/local/share/julia"
 }
 
-// Capture exit codes from upstream processes when piping
-process.shell = ['/bin/bash', '-euo', 'pipefail']
+// Set bash options
+process.shell = """\
+bash
+
+set -e # Exit if a tool returns a non-zero status/exit code
+set -u # Treat unset variables and parameters as an error
+set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
+set -C # No clobber - prevent output redirection from overwriting files.
+"""
 
 // Disable process selector warnings by default. Use debug profile to enable warnings.
 nextflow.enable.configProcessNamesValidation = false
@@ -238,43 +220,47 @@ manifest {
     homePage        = 'https://github.com/nf-core/seqinspector'
     description     = """Pipeline to QC your sequences"""
     mainScript      = 'main.nf'
-    nextflowVersion = '!>=23.04.0'
+    nextflowVersion = '!>=24.04.2'
     version         = '1.0dev'
     doi             = ''
 }
 
-// Load modules.config for DSL2 module specific options
-includeConfig 'conf/modules.config'
+// Nextflow plugins
+plugins {
+    id 'nf-schema@2.1.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+}
+
+validation {
+    defaultIgnoreParams = ["genomes"]
+    help {
+        enabled = true
+        command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
+        fullParameter = "help_full"
+        showHiddenParameter = "show_hidden"
+        beforeText = """
+-\033[2m----------------------------------------------------\033[0m-
+                                        \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m
+\033[0;34m        ___     __   __   __   ___     \033[0;32m/,-._.--~\'\033[0m
+\033[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \033[0;33m}  {\033[0m
+\033[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \033[0;32m\\`-._,-`-,\033[0m
+                                        \033[0;32m`._,._,\'\033[0m
+\033[0;35m  ${manifest.name} ${manifest.version}\033[0m
+-\033[2m----------------------------------------------------\033[0m-
+"""
+        afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "  https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
+* The nf-core framework
+  https://doi.org/10.1038/s41587-020-0439-x
 
-// Function to ensure that resource requirements don't go beyond
-// a maximum limit
-def check_max(obj, type) {
-    if (type == 'memory') {
-        try {
-            if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
-                return params.max_memory as nextflow.util.MemoryUnit
-            else
-                return obj
-        } catch (all) {
-            println "   ### ERROR ###   Max memory '${params.max_memory}' is not valid! Using default value: $obj"
-            return obj
-        }
-    } else if (type == 'time') {
-        try {
-            if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
-                return params.max_time as nextflow.util.Duration
-            else
-                return obj
-        } catch (all) {
-            println "   ### ERROR ###   Max time '${params.max_time}' is not valid! Using default value: $obj"
-            return obj
-        }
-    } else if (type == 'cpus') {
-        try {
-            return Math.min( obj, params.max_cpus as int )
-        } catch (all) {
-            println "   ### ERROR ###   Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
-            return obj
-        }
+* Software dependencies
+  https://github.com/${manifest.name}/blob/master/CITATIONS.md
+"""
+    }
+    summary {
+        beforeText = validation.help.beforeText
+        afterText = validation.help.afterText
     }
 }
+
+// Load modules.config for DSL2 module specific options
+includeConfig 'conf/modules.config'
+
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 36308a0..88fd607 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -1,10 +1,10 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "$id": "https://raw.githubusercontent.com/nf-core/seqinspector/master/nextflow_schema.json",
     "title": "nf-core/seqinspector pipeline parameters",
     "description": "Pipeline to QC your sequences",
     "type": "object",
-    "definitions": {
+    "$defs": {
         "input_output_options": {
             "title": "Input/output options",
             "type": "object",
@@ -71,6 +71,14 @@
                     "fa_icon": "fas fa-ban",
                     "hidden": true,
                     "help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`."
+                },
+                "igenomes_base": {
+                    "type": "string",
+                    "format": "directory-path",
+                    "description": "The base path to the igenomes reference files",
+                    "fa_icon": "fas fa-ban",
+                    "hidden": true,
+                    "default": "s3://ngi-igenomes/igenomes/"
                 }
             }
         },
@@ -122,41 +130,6 @@
                 }
             }
         },
-        "max_job_request_options": {
-            "title": "Max job request options",
-            "type": "object",
-            "fa_icon": "fab fa-acquisitions-incorporated",
-            "description": "Set the top limit for requested resources for any single job.",
-            "help_text": "If you are running on a smaller system, a pipeline step requesting more resources than are available may cause the Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system.\n\nNote that you can not _increase_ the resources requested by any job using these options. For that you will need your own configuration file. See [the nf-core website](https://nf-co.re/usage/configuration) for details.",
-            "properties": {
-                "max_cpus": {
-                    "type": "integer",
-                    "description": "Maximum number of CPUs that can be requested for any single job.",
-                    "default": 16,
-                    "fa_icon": "fas fa-microchip",
-                    "hidden": true,
-                    "help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`"
-                },
-                "max_memory": {
-                    "type": "string",
-                    "description": "Maximum amount of memory that can be requested for any single job.",
-                    "default": "128.GB",
-                    "fa_icon": "fas fa-memory",
-                    "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
-                    "hidden": true,
-                    "help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`"
-                },
-                "max_time": {
-                    "type": "string",
-                    "description": "Maximum amount of time that can be requested for any single job.",
-                    "default": "240.h",
-                    "fa_icon": "far fa-clock",
-                    "pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$",
-                    "hidden": true,
-                    "help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`"
-                }
-            }
-        },
         "generic_options": {
             "title": "Generic options",
             "type": "object",
@@ -164,12 +137,6 @@
             "description": "Less common options for the pipeline, typically set in a config file.",
             "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
             "properties": {
-                "help": {
-                    "type": "boolean",
-                    "description": "Display help text.",
-                    "fa_icon": "fas fa-question-circle",
-                    "hidden": true
-                },
                 "version": {
                     "type": "boolean",
                     "description": "Display version and exit.",
@@ -245,27 +212,6 @@
                     "fa_icon": "fas fa-check-square",
                     "hidden": true
                 },
-                "validationShowHiddenParams": {
-                    "type": "boolean",
-                    "fa_icon": "far fa-eye-slash",
-                    "description": "Show all params when using `--help`",
-                    "hidden": true,
-                    "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
-                },
-                "validationFailUnrecognisedParams": {
-                    "type": "boolean",
-                    "fa_icon": "far fa-check-circle",
-                    "description": "Validation of parameters fails when an unrecognised parameter is found.",
-                    "hidden": true,
-                    "help_text": "By default, when an unrecognised parameter is found, it returns a warinig."
-                },
-                "validationLenientMode": {
-                    "type": "boolean",
-                    "fa_icon": "far fa-check-circle",
-                    "description": "Validation of parameters in lenient more.",
-                    "hidden": true,
-                    "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)."
-                },
                 "pipelines_testdata_base_path": {
                     "type": "string",
                     "fa_icon": "far fa-check-circle",
@@ -278,19 +224,16 @@
     },
     "allOf": [
         {
-            "$ref": "#/definitions/input_output_options"
-        },
-        {
-            "$ref": "#/definitions/reference_genome_options"
+            "$ref": "#/$defs/input_output_options"
         },
         {
-            "$ref": "#/definitions/institutional_config_options"
+            "$ref": "#/$defs/reference_genome_options"
         },
         {
-            "$ref": "#/definitions/max_job_request_options"
+            "$ref": "#/$defs/institutional_config_options"
         },
         {
-            "$ref": "#/definitions/generic_options"
+            "$ref": "#/$defs/generic_options"
         }
     ]
 }
diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index 8728141..2571a5f 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -8,17 +8,14 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin'
-include { paramsSummaryMap          } from 'plugin/nf-validation'
-include { fromSamplesheet           } from 'plugin/nf-validation'
-include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
+include { UTILS_NFSCHEMA_PLUGIN     } from '../../nf-core/utils_nfschema_plugin'
+include { paramsSummaryMap          } from 'plugin/nf-schema'
+include { samplesheetToList         } from 'plugin/nf-schema'
 include { completionEmail           } from '../../nf-core/utils_nfcore_pipeline'
 include { completionSummary         } from '../../nf-core/utils_nfcore_pipeline'
-include { dashedLine                } from '../../nf-core/utils_nfcore_pipeline'
-include { nfCoreLogo                } from '../../nf-core/utils_nfcore_pipeline'
 include { imNotification            } from '../../nf-core/utils_nfcore_pipeline'
 include { UTILS_NFCORE_PIPELINE     } from '../../nf-core/utils_nfcore_pipeline'
-include { workflowCitation          } from '../../nf-core/utils_nfcore_pipeline'
+include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
 
 /*
 ========================================================================================
@@ -30,7 +27,6 @@ workflow PIPELINE_INITIALISATION {
 
     take:
     version           // boolean: Display version and exit
-    help              // boolean: Display help text
     validate_params   // boolean: Boolean whether to validate parameters against the schema at runtime
     monochrome_logs   // boolean: Do not use coloured log outputs
     nextflow_cli_args //   array: List of positional nextflow CLI args
@@ -51,20 +47,16 @@ workflow PIPELINE_INITIALISATION {
         workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1
     )
 
+    
     //
     // Validate parameters and generate parameter summary to stdout
     //
-    pre_help_text = nfCoreLogo(monochrome_logs)
-    post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(monochrome_logs)
-    def String workflow_command = "nextflow run ${workflow.manifest.name} -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
-    UTILS_NFVALIDATION_PLUGIN (
-        help,
-        workflow_command,
-        pre_help_text,
-        post_help_text,
+    UTILS_NFSCHEMA_PLUGIN (
+        workflow,
         validate_params,
-        "nextflow_schema.json"
+        null
     )
+    
 
     //
     // Check config provided to the pipeline
@@ -80,8 +72,9 @@ workflow PIPELINE_INITIALISATION {
     //
     // Create channel from input file provided through params.input
     //
+
     Channel
-        .fromSamplesheet("input")
+        .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
         .map {
             meta, fastq_1, fastq_2 ->
                 if (!fastq_2) {
@@ -91,8 +84,8 @@ workflow PIPELINE_INITIALISATION {
                 }
         }
         .groupTuple()
-        .map {
-            validateInputSamplesheet(it)
+        .map { samplesheet ->
+            validateInputSamplesheet(samplesheet)
         }
         .map {
             meta, fastqs ->
@@ -117,13 +110,13 @@ workflow PIPELINE_COMPLETION {
     email           //  string: email address
     email_on_fail   //  string: email address sent on pipeline failure
     plaintext_email // boolean: Send plain-text email instead of HTML
+    
     outdir          //    path: Path to output directory where results will be published
     monochrome_logs // boolean: Disable ANSI colour codes in log output
     hook_url        //  string: hook URL for notifications
     multiqc_report  //  string: Path to MultiQC report
 
     main:
-
     summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
 
     //
@@ -131,11 +124,18 @@ workflow PIPELINE_COMPLETION {
     //
     workflow.onComplete {
         if (email || email_on_fail) {
-            completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, multiqc_report.toList())
+            completionEmail(
+                summary_params,
+                email,
+                email_on_fail,
+                plaintext_email,
+                outdir,
+                monochrome_logs,
+                multiqc_report.toList()
+            )
         }
 
         completionSummary(monochrome_logs)
-
         if (hook_url) {
             imNotification(summary_params, hook_url)
         }
@@ -165,7 +165,7 @@ def validateInputSamplesheet(input) {
     def (metas, fastqs) = input[1..2]
 
     // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end
-    def endedness_ok = metas.collect{ it.single_end }.unique().size == 1
+    def endedness_ok = metas.collect{ meta -> meta.single_end }.unique().size == 1
     if (!endedness_ok) {
         error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}")
     }
@@ -197,7 +197,6 @@ def genomeExistsError() {
         error(error_string)
     }
 }
-
 //
 // Generate methods description for MultiQC
 //
@@ -239,8 +238,10 @@ def methodsDescriptionText(mqc_methods_yaml) {
         // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
         // Removing ` ` since the manifest.doi is a string and not a proper list
         def temp_doi_ref = ""
-        String[] manifest_doi = meta.manifest_map.doi.tokenize(",")
-        for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: <a href=\'https://doi.org/${doi_ref.replace("https://doi.org/", "").replace(" ", "")}\'>${doi_ref.replace("https://doi.org/", "").replace(" ", "")}</a>), "
+        def manifest_doi = meta.manifest_map.doi.tokenize(",")
+        manifest_doi.each { doi_ref ->
+            temp_doi_ref += "(doi: <a href=\'https://doi.org/${doi_ref.replace("https://doi.org/", "").replace(" ", "")}\'>${doi_ref.replace("https://doi.org/", "").replace(" ", "")}</a>), "
+        }
         meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length() - 2)
     } else meta["doi_text"] = ""
     meta["nodoi_text"] = meta.manifest_map.doi ? "" : "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"
@@ -261,3 +262,4 @@ def methodsDescriptionText(mqc_methods_yaml) {
 
     return description_html.toString()
 }
+
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
index ac31f28..28e32b2 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
@@ -2,10 +2,6 @@
 // Subworkflow with functionality that may be useful for any Nextflow pipeline
 //
 
-import org.yaml.snakeyaml.Yaml
-import groovy.json.JsonOutput
-import nextflow.extension.FilesEx
-
 /*
 ========================================================================================
     SUBWORKFLOW DEFINITION
@@ -58,7 +54,7 @@ workflow UTILS_NEXTFLOW_PIPELINE {
 // Generate version string
 //
 def getWorkflowVersion() {
-    String version_string = ""
+    def version_string = "" as String
     if (workflow.manifest.version) {
         def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
         version_string += "${prefix_v}${workflow.manifest.version}"
@@ -79,10 +75,10 @@ def dumpParametersToJSON(outdir) {
     def timestamp  = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
     def filename   = "params_${timestamp}.json"
     def temp_pf    = new File(workflow.launchDir.toString(), ".${filename}")
-    def jsonStr    = JsonOutput.toJson(params)
-    temp_pf.text   = JsonOutput.prettyPrint(jsonStr)
+    def jsonStr    = groovy.json.JsonOutput.toJson(params)
+    temp_pf.text   = groovy.json.JsonOutput.prettyPrint(jsonStr)
 
-    FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json")
+    nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json")
     temp_pf.delete()
 }
 
@@ -90,7 +86,7 @@ def dumpParametersToJSON(outdir) {
 // When running with -profile conda, warn if channels have not been set-up appropriately
 //
 def checkCondaChannels() {
-    Yaml parser = new Yaml()
+    def parser = new org.yaml.snakeyaml.Yaml()
     def channels = []
     try {
         def config = parser.load("conda config --show channels".execute().text)
@@ -102,14 +98,16 @@ def checkCondaChannels() {
 
     // Check that all channels are present
     // This channel list is ordered by required channel priority.
-    def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults']
+    def required_channels_in_order = ['conda-forge', 'bioconda']
     def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean
 
     // Check that they are in the right order
     def channel_priority_violation = false
-    def n = required_channels_in_order.size()
-    for (int i = 0; i < n - 1; i++) {
-        channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1]))
+
+    required_channels_in_order.eachWithIndex { channel, index ->
+        if (index < required_channels_in_order.size() - 1) {
+            channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index+1]))
+        }
     }
 
     if (channels_missing | channel_priority_violation) {
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
index d0a926b..a09572e 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
@@ -3,7 +3,7 @@ manifest {
     author          = """nf-core"""
     homePage        = 'https://127.0.0.1'
     description     = """Dummy pipeline"""
-    nextflowVersion  = '!>=23.04.0'
+    nextflowVersion = '!>=23.04.0'
     version         = '9.9.9'
     doi             = 'https://doi.org/10.5281/zenodo.5070524'
 }
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index 14558c3..cbd8495 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -2,9 +2,6 @@
 // Subworkflow with utility functions specific to the nf-core pipeline template
 //
 
-import org.yaml.snakeyaml.Yaml
-import nextflow.extension.FilesEx
-
 /*
 ========================================================================================
     SUBWORKFLOW DEFINITION
@@ -34,7 +31,7 @@ workflow UTILS_NFCORE_PIPELINE {
 //  Warn if a -profile or Nextflow config has not been provided to run the pipeline
 //
 def checkConfigProvided() {
-    valid_config = true
+    def valid_config = true as Boolean
     if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) {
         log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" +
             "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" +
@@ -66,11 +63,13 @@ def checkProfileProvided(nextflow_cli_args) {
 //
 def workflowCitation() {
     def temp_doi_ref = ""
-    String[] manifest_doi = workflow.manifest.doi.tokenize(",")
+    def manifest_doi = workflow.manifest.doi.tokenize(",")
     // Using a loop to handle multiple DOIs
     // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
     // Removing ` ` since the manifest.doi is a string and not a proper list
-    for (String doi_ref: manifest_doi) temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
+    manifest_doi.each { doi_ref ->
+        temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
+    }
     return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
         "* The pipeline\n" +
         temp_doi_ref + "\n" +
@@ -84,7 +83,7 @@ def workflowCitation() {
 // Generate workflow version string
 //
 def getWorkflowVersion() {
-    String version_string = ""
+    def version_string = "" as String
     if (workflow.manifest.version) {
         def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
         version_string += "${prefix_v}${workflow.manifest.version}"
@@ -102,8 +101,8 @@ def getWorkflowVersion() {
 // Get software versions for pipeline
 //
 def processVersionsFromYAML(yaml_file) {
-    Yaml yaml = new Yaml()
-    versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] }
+    def yaml = new org.yaml.snakeyaml.Yaml()
+    def versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] }
     return yaml.dumpAsMap(versions).trim()
 }
 
@@ -124,7 +123,7 @@ def workflowVersionToYAML() {
 def softwareVersionsToYAML(ch_versions) {
     return ch_versions
                 .unique()
-                .map { processVersionsFromYAML(it) }
+                .map { version -> processVersionsFromYAML(version) }
                 .unique()
                 .mix(Channel.of(workflowVersionToYAML()))
 }
@@ -134,19 +133,19 @@ def softwareVersionsToYAML(ch_versions) {
 //
 def paramsSummaryMultiqc(summary_params) {
     def summary_section = ''
-    for (group in summary_params.keySet()) {
+    summary_params.keySet().each { group ->
         def group_params = summary_params.get(group)  // This gets the parameters of that particular group
         if (group_params) {
             summary_section += "    <p style=\"font-size:110%\"><b>$group</b></p>\n"
             summary_section += "    <dl class=\"dl-horizontal\">\n"
-            for (param in group_params.keySet()) {
+            group_params.keySet().sort().each { param ->
                 summary_section += "        <dt>$param</dt><dd><samp>${group_params.get(param) ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>\n"
             }
             summary_section += "    </dl>\n"
         }
     }
 
-    String yaml_file_text  = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n"
+    def yaml_file_text  = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" as String
     yaml_file_text        += "description: ' - this information is collected when the pipeline is started.'\n"
     yaml_file_text        += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
     yaml_file_text        += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
@@ -161,7 +160,7 @@ def paramsSummaryMultiqc(summary_params) {
 // nf-core logo
 //
 def nfCoreLogo(monochrome_logs=true) {
-    Map colors = logColours(monochrome_logs)
+    def colors = logColours(monochrome_logs) as Map
     String.format(
         """\n
         ${dashedLine(monochrome_logs)}
@@ -180,7 +179,7 @@ def nfCoreLogo(monochrome_logs=true) {
 // Return dashed line
 //
 def dashedLine(monochrome_logs=true) {
-    Map colors = logColours(monochrome_logs)
+    def colors = logColours(monochrome_logs) as Map
     return "-${colors.dim}----------------------------------------------------${colors.reset}-"
 }
 
@@ -188,7 +187,7 @@ def dashedLine(monochrome_logs=true) {
 // ANSII colours used for terminal logging
 //
 def logColours(monochrome_logs=true) {
-    Map colorcodes = [:]
+    def colorcodes = [:] as Map
 
     // Reset / Meta
     colorcodes['reset']      = monochrome_logs ? '' : "\033[0m"
@@ -287,7 +286,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     }
 
     def summary = [:]
-    for (group in summary_params.keySet()) {
+    summary_params.keySet().sort().each { group ->
         summary << summary_params[group]
     }
 
@@ -344,10 +343,10 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     def sendmail_html          = sendmail_template.toString()
 
     // Send the HTML e-mail
-    Map colors = logColours(monochrome_logs)
+    def colors = logColours(monochrome_logs) as Map
     if (email_address) {
         try {
-            if (plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
+            if (plaintext_email) { throw new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') }
             // Try to send HTML e-mail using sendmail
             def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html")
             sendmail_tf.withWriter { w -> w << sendmail_html }
@@ -364,13 +363,13 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     // Write summary e-mail HTML to a file
     def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html")
     output_hf.withWriter { w -> w << email_html }
-    FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html");
+    nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html");
     output_hf.delete()
 
     // Write summary e-mail TXT to a file
     def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt")
     output_tf.withWriter { w -> w << email_txt }
-    FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt");
+    nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt");
     output_tf.delete()
 }
 
@@ -378,7 +377,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
 // Print pipeline summary on completion
 //
 def completionSummary(monochrome_logs=true) {
-    Map colors = logColours(monochrome_logs)
+    def colors = logColours(monochrome_logs) as Map
     if (workflow.success) {
         if (workflow.stats.ignoredCount == 0) {
             log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-"
@@ -395,7 +394,7 @@ def completionSummary(monochrome_logs=true) {
 //
 def imNotification(summary_params, hook_url) {
     def summary = [:]
-    for (group in summary_params.keySet()) {
+    summary_params.keySet().sort().each { group ->
         summary << summary_params[group]
     }
 
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf
new file mode 100644
index 0000000..4994303
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf
@@ -0,0 +1,46 @@
+//
+// Subworkflow that uses the nf-schema plugin to validate parameters and render the parameter summary
+//
+
+include { paramsSummaryLog   } from 'plugin/nf-schema'
+include { validateParameters } from 'plugin/nf-schema'
+
+workflow UTILS_NFSCHEMA_PLUGIN {
+
+    take:
+    input_workflow      // workflow: the workflow object used by nf-schema to get metadata from the workflow
+    validate_params     // boolean:  validate the parameters
+    parameters_schema   // string:   path to the parameters JSON schema.
+                        //           this has to be the same as the schema given to `validation.parametersSchema`
+                        //           when this input is empty it will automatically use the configured schema or
+                        //           "${projectDir}/nextflow_schema.json" as default. This input should not be empty
+                        //           for meta pipelines
+
+    main:
+
+    //
+    // Print parameter summary to stdout. This will display the parameters
+    // that differ from the default given in the JSON schema
+    //
+    if(parameters_schema) {
+        log.info paramsSummaryLog(input_workflow, parameters_schema:parameters_schema)
+    } else {
+        log.info paramsSummaryLog(input_workflow)
+    }
+
+    //
+    // Validate the parameters using nextflow_schema.json or the schema
+    // given via the validation.parametersSchema configuration option
+    //
+    if(validate_params) {
+        if(parameters_schema) {
+            validateParameters(parameters_schema:parameters_schema)
+        } else {
+            validateParameters()
+        }
+    }
+
+    emit:
+    dummy_emit = true
+}
+
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/meta.yml b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml
new file mode 100644
index 0000000..f7d9f02
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml
@@ -0,0 +1,35 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "utils_nfschema_plugin"
+description: Run nf-schema to validate parameters and create a summary of changed parameters
+keywords:
+  - validation
+  - JSON schema
+  - plugin
+  - parameters
+  - summary
+components: []
+input:
+  - input_workflow:
+      type: object
+      description: |
+        The workflow object of the used pipeline.
+        This object contains meta data used to create the params summary log
+  - validate_params:
+      type: boolean
+      description: Validate the parameters and error if invalid.
+  - parameters_schema:
+      type: string
+      description: |
+        Path to the parameters JSON schema.
+        This has to be the same as the schema given to the `validation.parametersSchema` config
+        option. When this input is empty it will automatically use the configured schema or
+        "${projectDir}/nextflow_schema.json" as default. The schema should not be given in this way
+        for meta pipelines.
+output:
+  - dummy_emit:
+      type: boolean
+      description: Dummy emit to make nf-core subworkflows lint happy
+authors:
+  - "@nvnieuwk"
+maintainers:
+  - "@nvnieuwk"
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
new file mode 100644
index 0000000..842dc43
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
@@ -0,0 +1,117 @@
+nextflow_workflow {
+
+    name "Test Subworkflow UTILS_NFSCHEMA_PLUGIN"
+    script "../main.nf"
+    workflow "UTILS_NFSCHEMA_PLUGIN"
+
+    tag "subworkflows"
+    tag "subworkflows_nfcore"
+    tag "subworkflows/utils_nfschema_plugin"
+    tag "plugin/nf-schema"
+
+    config "./nextflow.config"
+
+    test("Should run nothing") {
+
+        when {
+
+            params {
+                test_data   = ''
+            }
+
+            workflow {
+                """
+                validate_params = false
+                input[0] = workflow
+                input[1] = validate_params
+                input[2] = ""
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+
+    test("Should validate params") {
+
+        when {
+
+            params {
+                test_data   = ''
+                outdir      = 1
+            }
+
+            workflow {
+                """
+                validate_params = true
+                input[0] = workflow
+                input[1] = validate_params
+                input[2] = ""
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.failed },
+                { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } }
+            )
+        }
+    }
+
+    test("Should run nothing - custom schema") {
+
+        when {
+
+            params {
+                test_data   = ''
+            }
+
+            workflow {
+                """
+                validate_params = false
+                input[0] = workflow
+                input[1] = validate_params
+                input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+
+    test("Should validate params - custom schema") {
+
+        when {
+
+            params {
+                test_data   = ''
+                outdir      = 1
+            }
+
+            workflow {
+                """
+                validate_params = true
+                input[0] = workflow
+                input[1] = validate_params
+                input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.failed },
+                { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } }
+            )
+        }
+    }
+}
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
new file mode 100644
index 0000000..0907ac5
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
@@ -0,0 +1,8 @@
+plugins {
+    id "nf-schema@2.1.0"
+}
+
+validation {
+    parametersSchema = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
+    monochromeLogs = true
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json
similarity index 95%
rename from subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json
rename to subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json
index 7626c1c..331e0d2 100644
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json
@@ -1,10 +1,10 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json",
     "title": ". pipeline parameters",
     "description": "",
     "type": "object",
-    "definitions": {
+    "$defs": {
         "input_output_options": {
             "title": "Input/output options",
             "type": "object",
@@ -87,10 +87,10 @@
     },
     "allOf": [
         {
-            "$ref": "#/definitions/input_output_options"
+            "$ref": "#/$defs/input_output_options"
         },
         {
-            "$ref": "#/definitions/generic_options"
+            "$ref": "#/$defs/generic_options"
         }
     ]
 }
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
deleted file mode 100644
index 2585b65..0000000
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
+++ /dev/null
@@ -1,62 +0,0 @@
-//
-// Subworkflow that uses the nf-validation plugin to render help text and parameter summary
-//
-
-/*
-========================================================================================
-    IMPORT NF-VALIDATION PLUGIN
-========================================================================================
-*/
-
-include { paramsHelp         } from 'plugin/nf-validation'
-include { paramsSummaryLog   } from 'plugin/nf-validation'
-include { validateParameters } from 'plugin/nf-validation'
-
-/*
-========================================================================================
-    SUBWORKFLOW DEFINITION
-========================================================================================
-*/
-
-workflow UTILS_NFVALIDATION_PLUGIN {
-
-    take:
-    print_help       // boolean: print help
-    workflow_command //  string: default commmand used to run pipeline
-    pre_help_text    //  string: string to be printed before help text and summary log
-    post_help_text   //  string: string to be printed after help text and summary log
-    validate_params  // boolean: validate parameters
-    schema_filename  //    path: JSON schema file, null to use default value
-
-    main:
-
-    log.debug "Using schema file: ${schema_filename}"
-
-    // Default values for strings
-    pre_help_text    = pre_help_text    ?: ''
-    post_help_text   = post_help_text   ?: ''
-    workflow_command = workflow_command ?: ''
-
-    //
-    // Print help message if needed
-    //
-    if (print_help) {
-        log.info pre_help_text + paramsHelp(workflow_command, parameters_schema: schema_filename) + post_help_text
-        System.exit(0)
-    }
-
-    //
-    // Print parameter summary to stdout
-    //
-    log.info pre_help_text + paramsSummaryLog(workflow, parameters_schema: schema_filename) + post_help_text
-
-    //
-    // Validate parameters relative to the parameter JSON schema
-    //
-    if (validate_params){
-        validateParameters(parameters_schema: schema_filename)
-    }
-
-    emit:
-    dummy_emit = true
-}
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml
deleted file mode 100644
index 3d4a6b0..0000000
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml
+++ /dev/null
@@ -1,44 +0,0 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
-name: "UTILS_NFVALIDATION_PLUGIN"
-description: Use nf-validation to initiate and validate a pipeline
-keywords:
-  - utility
-  - pipeline
-  - initialise
-  - validation
-components: []
-input:
-  - print_help:
-      type: boolean
-      description: |
-        Print help message and exit
-  - workflow_command:
-      type: string
-      description: |
-        The command to run the workflow e.g. "nextflow run main.nf"
-  - pre_help_text:
-      type: string
-      description: |
-        Text to print before the help message
-  - post_help_text:
-      type: string
-      description: |
-        Text to print after the help message
-  - validate_params:
-      type: boolean
-      description: |
-        Validate the parameters and error if invalid.
-  - schema_filename:
-      type: string
-      description: |
-        The filename of the schema to validate against.
-output:
-  - dummy_emit:
-      type: boolean
-      description: |
-        Dummy emit to make nf-core subworkflows lint happy
-authors:
-  - "@adamrtalbot"
-maintainers:
-  - "@adamrtalbot"
-  - "@maxulysse"
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
deleted file mode 100644
index 5784a33..0000000
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
+++ /dev/null
@@ -1,200 +0,0 @@
-nextflow_workflow {
-
-    name "Test Workflow UTILS_NFVALIDATION_PLUGIN"
-    script "../main.nf"
-    workflow "UTILS_NFVALIDATION_PLUGIN"
-    tag "subworkflows"
-    tag "subworkflows_nfcore"
-    tag "plugin/nf-validation"
-    tag "'plugin/nf-validation'"
-    tag "utils_nfvalidation_plugin"
-    tag "subworkflows/utils_nfvalidation_plugin"
-
-    test("Should run nothing") {
-
-        when {
-
-            params {
-                monochrome_logs = true
-                test_data       = ''
-            }
-
-            workflow {
-                """
-                help             = false
-                workflow_command = null
-                pre_help_text    = null
-                post_help_text   = null
-                validate_params  = false
-                schema_filename  = "$moduleTestDir/nextflow_schema.json"
-
-                input[0] = help
-                input[1] = workflow_command
-                input[2] = pre_help_text
-                input[3] = post_help_text
-                input[4] = validate_params
-                input[5] = schema_filename
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success }
-            )
-        }
-    }
-
-    test("Should run help") {
-
-
-        when {
-
-            params {
-                monochrome_logs = true
-                test_data       = ''
-            }
-            workflow {
-                """
-                help             = true
-                workflow_command = null
-                pre_help_text    = null
-                post_help_text   = null
-                validate_params  = false
-                schema_filename  = "$moduleTestDir/nextflow_schema.json"
-
-                input[0] = help
-                input[1] = workflow_command
-                input[2] = pre_help_text
-                input[3] = post_help_text
-                input[4] = validate_params
-                input[5] = schema_filename
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert workflow.exitStatus == 0 },
-                { assert workflow.stdout.any { it.contains('Input/output options') } },
-                { assert workflow.stdout.any { it.contains('--outdir') } }
-            )
-        }
-    }
-
-    test("Should run help with command") {
-
-        when {
-
-            params {
-                monochrome_logs = true
-                test_data       = ''
-            }
-            workflow {
-                """
-                help             = true
-                workflow_command = "nextflow run noorg/doesntexist"
-                pre_help_text    = null
-                post_help_text   = null
-                validate_params  = false
-                schema_filename  = "$moduleTestDir/nextflow_schema.json"
-
-                input[0] = help
-                input[1] = workflow_command
-                input[2] = pre_help_text
-                input[3] = post_help_text
-                input[4] = validate_params
-                input[5] = schema_filename
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert workflow.exitStatus == 0 },
-                { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } },
-                { assert workflow.stdout.any { it.contains('Input/output options') } },
-                { assert workflow.stdout.any { it.contains('--outdir') } }
-            )
-        }
-    }
-
-    test("Should run help with extra text") {
-
-
-        when {
-
-            params {
-                monochrome_logs = true
-                test_data       = ''
-            }
-            workflow {
-                """
-                help             = true
-                workflow_command = "nextflow run noorg/doesntexist"
-                pre_help_text    = "pre-help-text"
-                post_help_text   = "post-help-text"
-                validate_params  = false
-                schema_filename  = "$moduleTestDir/nextflow_schema.json"
-
-                input[0] = help
-                input[1] = workflow_command
-                input[2] = pre_help_text
-                input[3] = post_help_text
-                input[4] = validate_params
-                input[5] = schema_filename
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert workflow.exitStatus == 0 },
-                { assert workflow.stdout.any { it.contains('pre-help-text') } },
-                { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } },
-                { assert workflow.stdout.any { it.contains('Input/output options') } },
-                { assert workflow.stdout.any { it.contains('--outdir') } },
-                { assert workflow.stdout.any { it.contains('post-help-text') } }
-            )
-        }
-    }
-
-    test("Should validate params") {
-
-        when {
-
-            params {
-                monochrome_logs = true
-                test_data       = ''
-                outdir          = 1
-            }
-            workflow {
-                """
-                help             = false
-                workflow_command = null
-                pre_help_text    = null
-                post_help_text   = null
-                validate_params  = true
-                schema_filename  = "$moduleTestDir/nextflow_schema.json"
-
-                input[0] = help
-                input[1] = workflow_command
-                input[2] = pre_help_text
-                input[3] = post_help_text
-                input[4] = validate_params
-                input[5] = schema_filename
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.failed },
-                { assert workflow.stdout.any { it.contains('ERROR ~ ERROR: Validation of pipeline parameters failed!') } }
-            )
-        }
-    }
-}
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml
deleted file mode 100644
index 60b1cff..0000000
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-subworkflows/utils_nfvalidation_plugin:
-  - subworkflows/nf-core/utils_nfvalidation_plugin/**
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index cf7a85c..af3719c 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -3,10 +3,9 @@
     IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
-
 include { FASTQC                 } from '../modules/nf-core/fastqc/main'
 include { MULTIQC                } from '../modules/nf-core/multiqc/main'
-include { paramsSummaryMap       } from 'plugin/nf-validation'
+include { paramsSummaryMap       } from 'plugin/nf-schema'
 include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_seqinspector_pipeline'
@@ -21,12 +20,10 @@ workflow SEQINSPECTOR {
 
     take:
     ch_samplesheet // channel: samplesheet read in from --input
-
     main:
 
     ch_versions = Channel.empty()
     ch_multiqc_files = Channel.empty()
-
     //
     // MODULE: Run FastQC
     //
@@ -42,11 +39,12 @@ workflow SEQINSPECTOR {
     softwareVersionsToYAML(ch_versions)
         .collectFile(
             storeDir: "${params.outdir}/pipeline_info",
-            name: 'nf_core_pipeline_software_mqc_versions.yml',
+            name: 'nf_core_'  + 'pipeline_software_' +  'mqc_'  + 'versions.yml',
             sort: true,
             newLine: true
         ).set { ch_collated_versions }
 
+
     //
     // MODULE: MultiQC
     //
@@ -59,18 +57,19 @@ workflow SEQINSPECTOR {
         Channel.fromPath(params.multiqc_logo, checkIfExists: true) :
         Channel.empty()
 
+    
     summary_params      = paramsSummaryMap(
         workflow, parameters_schema: "nextflow_schema.json")
     ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
-
+    ch_multiqc_files = ch_multiqc_files.mix(
+        ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
+    
     ch_multiqc_custom_methods_description = params.multiqc_methods_description ?
         file(params.multiqc_methods_description, checkIfExists: true) :
         file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
     ch_methods_description                = Channel.value(
         methodsDescriptionText(ch_multiqc_custom_methods_description))
 
-    ch_multiqc_files = ch_multiqc_files.mix(
-        ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
     ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)
     ch_multiqc_files = ch_multiqc_files.mix(
         ch_methods_description.collectFile(
@@ -83,12 +82,14 @@ workflow SEQINSPECTOR {
         ch_multiqc_files.collect(),
         ch_multiqc_config.toList(),
         ch_multiqc_custom_config.toList(),
-        ch_multiqc_logo.toList()
+        ch_multiqc_logo.toList(),
+        [],
+        []
     )
 
-    emit:
-    multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html
+    emit:multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html
     versions       = ch_versions                 // channel: [ path(versions.yml) ]
+
 }
 
 /*

From d5d1a04b0b48531e74fa8e63f7a994f05dcd7cc8 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Wed, 9 Oct 2024 11:07:36 +0000
Subject: [PATCH 52/58] Template update for nf-core/tools version 3.0.1

---
 .editorconfig                                 |   4 -
 .github/CONTRIBUTING.md                       |   2 +-
 .github/workflows/awsfulltest.yml             |   6 +-
 .github/workflows/linting.yml                 |   4 +-
 .nf-core.yml                                  |   2 +-
 .prettierignore                               |   1 -
 docs/output.md                                |   1 -
 modules.json                                  |   6 +-
 modules/nf-core/multiqc/environment.yml       |   2 +-
 modules/nf-core/multiqc/main.nf               |   4 +-
 .../nf-core/multiqc/tests/main.nf.test.snap   |  26 +-
 nextflow.config                               |   8 +-
 .../main.nf                                   |  12 +-
 .../nf-core/utils_nextflow_pipeline/main.nf   |  46 ++-
 .../nf-core/utils_nfcore_pipeline/main.nf     | 279 ++++++++++--------
 15 files changed, 209 insertions(+), 194 deletions(-)

diff --git a/.editorconfig b/.editorconfig
index e105881..72dda28 100644
--- a/.editorconfig
+++ b/.editorconfig
@@ -11,7 +11,6 @@ indent_style = space
 [*.{md,yml,yaml,html,css,scss,js}]
 indent_size = 2
 
-
 # These files are edited and tested upstream in nf-core/modules
 [/modules/nf-core/**]
 charset = unset
@@ -26,12 +25,9 @@ insert_final_newline = unset
 trim_trailing_whitespace = unset
 indent_style = unset
 
-
-
 [/assets/email*]
 indent_size = unset
 
-
 # ignore python and markdown
 [*.{py,md}]
 indent_style = unset
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index 78893ac..4bcb559 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -90,7 +90,7 @@ Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json
 
 ### Default processes resource requirements
 
-Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
+Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
 
 The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block.
 
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index c9462a5..5fdd276 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -14,16 +14,18 @@ on:
 jobs:
   run-platform:
     name: Run AWS full tests
-    if: github.repository == 'nf-core/seqinspector' && github.event.review.state == 'approved'
+    # run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered
+    if: github.repository == 'nf-core/seqinspector' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
     runs-on: ubuntu-latest
     steps:
       - uses: octokit/request-action@v2.x
         id: check_approvals
         with:
-          route: GET /repos/${{ github.repository }}/pulls/${{ github.event.review.number }}/reviews
+          route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       - id: test_variables
+        if: github.event_name != 'workflow_dispatch'
         run: |
           JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'
           CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length')
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index b882838..a502573 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -42,10 +42,10 @@ jobs:
           architecture: "x64"
 
       - name: read .nf-core.yml
-        uses: pietrobolcato/action-read-yaml@1.0.0
+        uses: pietrobolcato/action-read-yaml@1.1.0
         id: read_yml
         with:
-          config: ${{ github.workspace }}/.nf-core.yaml
+          config: ${{ github.workspace }}/.nf-core.yml
 
       - name: Install dependencies
         run: |
diff --git a/.nf-core.yml b/.nf-core.yml
index ca26523..4e85672 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,6 +1,6 @@
 bump_version: null
 lint: null
-nf_core_version: 3.0.0
+nf_core_version: 3.0.1
 org_path: null
 repository_type: pipeline
 template:
diff --git a/.prettierignore b/.prettierignore
index 610e506..437d763 100644
--- a/.prettierignore
+++ b/.prettierignore
@@ -1,4 +1,3 @@
-
 email_template.html
 adaptivecard.json
 slackreport.json
diff --git a/docs/output.md b/docs/output.md
index 9184bd0..e8665e5 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -14,7 +14,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 - [FastQC](#fastqc) - Raw read QC
 - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
-
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
 ### FastQC
diff --git a/modules.json b/modules.json
index 0ab8a79..4178960 100644
--- a/modules.json
+++ b/modules.json
@@ -12,7 +12,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "b8d36829fa84b6e404364abff787e8b07f6d058c",
                         "installed_by": ["modules"]
                     }
                 }
@@ -21,12 +21,12 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352",
+                        "git_sha": "9d05360da397692321d377b6102d2fb22507c6ef",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab",
+                        "git_sha": "772684d9d66f37b650c8ba5146ac1ee3ecba2acb",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index f1cd99b..6f5b867 100644
--- a/modules/nf-core/multiqc/environment.yml
+++ b/modules/nf-core/multiqc/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::multiqc=1.24.1
+  - bioconda::multiqc=1.25.1
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index b9ccebd..9724d2f 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -3,8 +3,8 @@ process MULTIQC {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.25--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.25--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.25.1--pyhdfd78af_0' }"
 
     input:
     path  multiqc_files, stageAs: "?/*"
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
index b779e46..2fcbb5f 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -2,14 +2,14 @@
     "multiqc_versions_single": {
         "content": [
             [
-                "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd"
+                "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-10T12:41:34.562023"
+        "timestamp": "2024-10-02T17:51:46.317523"
     },
     "multiqc_stub": {
         "content": [
@@ -17,25 +17,25 @@
                 "multiqc_report.html",
                 "multiqc_data",
                 "multiqc_plots",
-                "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd"
+                "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-10T11:27:11.933869532"
+        "timestamp": "2024-10-02T17:52:20.680978"
     },
     "multiqc_versions_config": {
         "content": [
             [
-                "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd"
+                "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-10T11:26:56.709849369"
+        "timestamp": "2024-10-02T17:52:09.185842"
     }
-}
+}
\ No newline at end of file
diff --git a/nextflow.config b/nextflow.config
index 90df166..caea85a 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -12,10 +12,12 @@ params {
     // TODO nf-core: Specify your pipeline's command line flags
     // Input options
     input                      = null
+
     // References
     genome                     = null
     igenomes_base              = 's3://ngi-igenomes/igenomes/'
     igenomes_ignore            = false
+
     // MultiQC options
     multiqc_config             = null
     multiqc_title              = null
@@ -36,6 +38,7 @@ params {
     show_hidden                  = false
     version                      = false
     pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
+
     // Config options
     config_profile_name        = null
     config_profile_description = null
@@ -44,9 +47,9 @@ params {
     custom_config_base         = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
     config_profile_contact     = null
     config_profile_url         = null
+
     // Schema validation default options
     validate_params            = true
-    
 }
 
 // Load base.config by default for all pipelines
@@ -161,6 +164,7 @@ includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${pa
 // Load nf-core/seqinspector custom profiles from different institutions.
 // TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
 // includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/seqinspector.config" : "/dev/null"
+
 // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
 // Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
 // Set to your registry if you have a mirror of containers
@@ -172,6 +176,7 @@ charliecloud.registry = 'quay.io'
 
 // Load igenomes.config if required
 includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config'
+
 // Export these variables to prevent local Python/R libraries from conflicting with those in the container
 // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
 // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
@@ -263,4 +268,3 @@ validation {
 
 // Load modules.config for DSL2 module specific options
 includeConfig 'conf/modules.config'
-
diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index 2571a5f..b255821 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -18,9 +18,9 @@ include { UTILS_NFCORE_PIPELINE     } from '../../nf-core/utils_nfcore_pipeline'
 include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUBWORKFLOW TO INITIALISE PIPELINE
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow PIPELINE_INITIALISATION {
@@ -99,9 +99,9 @@ workflow PIPELINE_INITIALISATION {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUBWORKFLOW FOR PIPELINE COMPLETION
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow PIPELINE_COMPLETION {
@@ -147,9 +147,9 @@ workflow PIPELINE_COMPLETION {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     FUNCTIONS
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 //
 // Check and validate pipeline parameters
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
index 28e32b2..2b0dc67 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
@@ -3,13 +3,12 @@
 //
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUBWORKFLOW DEFINITION
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow UTILS_NEXTFLOW_PIPELINE {
-
     take:
     print_version        // boolean: print version
     dump_parameters      // boolean: dump parameters
@@ -22,7 +21,7 @@ workflow UTILS_NEXTFLOW_PIPELINE {
     // Print workflow version and exit on --version
     //
     if (print_version) {
-        log.info "${workflow.manifest.name} ${getWorkflowVersion()}"
+        log.info("${workflow.manifest.name} ${getWorkflowVersion()}")
         System.exit(0)
     }
 
@@ -45,9 +44,9 @@ workflow UTILS_NEXTFLOW_PIPELINE {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     FUNCTIONS
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 //
@@ -72,11 +71,11 @@ def getWorkflowVersion() {
 // Dump pipeline parameters to a JSON file
 //
 def dumpParametersToJSON(outdir) {
-    def timestamp  = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
-    def filename   = "params_${timestamp}.json"
-    def temp_pf    = new File(workflow.launchDir.toString(), ".${filename}")
-    def jsonStr    = groovy.json.JsonOutput.toJson(params)
-    temp_pf.text   = groovy.json.JsonOutput.prettyPrint(jsonStr)
+    def timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss')
+    def filename  = "params_${timestamp}.json"
+    def temp_pf   = new File(workflow.launchDir.toString(), ".${filename}")
+    def jsonStr   = groovy.json.JsonOutput.toJson(params)
+    temp_pf.text  = groovy.json.JsonOutput.prettyPrint(jsonStr)
 
     nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json")
     temp_pf.delete()
@@ -91,9 +90,14 @@ def checkCondaChannels() {
     try {
         def config = parser.load("conda config --show channels".execute().text)
         channels = config.channels
-    } catch(NullPointerException | IOException e) {
-        log.warn "Could not verify conda channel configuration."
-        return
+    }
+    catch (NullPointerException e) {
+        log.warn("Could not verify conda channel configuration.")
+        return null
+    }
+    catch (IOException e) {
+        log.warn("Could not verify conda channel configuration.")
+        return null
     }
 
     // Check that all channels are present
@@ -106,19 +110,13 @@ def checkCondaChannels() {
 
     required_channels_in_order.eachWithIndex { channel, index ->
         if (index < required_channels_in_order.size() - 1) {
-            channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index+1]))
+            channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index + 1]))
         }
     }
 
     if (channels_missing | channel_priority_violation) {
-        log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
-            "  There is a problem with your Conda configuration!\n\n" +
-            "  You will need to set-up the conda-forge and bioconda channels correctly.\n" +
-            "  Please refer to https://bioconda.github.io/\n" +
-            "  The observed channel order is \n" +
-            "  ${channels}\n" +
-            "  but the following channel order is required:\n" +
-            "  ${required_channels_in_order}\n" +
-            "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+        log.warn(
+            "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + "  There is a problem with your Conda configuration!\n\n" + "  You will need to set-up the conda-forge and bioconda channels correctly.\n" + "  Please refer to https://bioconda.github.io/\n" + "  The observed channel order is \n" + "  ${channels}\n" + "  but the following channel order is required:\n" + "  ${required_channels_in_order}\n" + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+        )
     }
 }
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index cbd8495..b78273c 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -3,13 +3,12 @@
 //
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUBWORKFLOW DEFINITION
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow UTILS_NFCORE_PIPELINE {
-
     take:
     nextflow_cli_args
 
@@ -22,9 +21,9 @@ workflow UTILS_NFCORE_PIPELINE {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     FUNCTIONS
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 //
@@ -33,12 +32,9 @@ workflow UTILS_NFCORE_PIPELINE {
 def checkConfigProvided() {
     def valid_config = true as Boolean
     if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) {
-        log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" +
-            "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" +
-            "   (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" +
-            "   (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" +
-            "   (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" +
-            "Please refer to the quick start section and usage docs for the pipeline.\n "
+        log.warn(
+            "[${workflow.manifest.name}] You are attempting to run the pipeline without any custom configuration!\n\n" + "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + "   (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + "   (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + "   (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + "Please refer to the quick start section and usage docs for the pipeline.\n "
+        )
         valid_config = false
     }
     return valid_config
@@ -49,12 +45,14 @@ def checkConfigProvided() {
 //
 def checkProfileProvided(nextflow_cli_args) {
     if (workflow.profile.endsWith(',')) {
-        error "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" +
-            "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n"
+        error(
+            "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n"
+        )
     }
     if (nextflow_cli_args[0]) {
-        log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" +
-            "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n"
+        log.warn(
+            "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n"
+        )
     }
 }
 
@@ -70,13 +68,7 @@ def workflowCitation() {
     manifest_doi.each { doi_ref ->
         temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
     }
-    return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
-        "* The pipeline\n" +
-        temp_doi_ref + "\n" +
-        "* The nf-core framework\n" +
-        "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
-        "* Software dependencies\n" +
-        "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
+    return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + "* The pipeline\n" + temp_doi_ref + "\n" + "* The nf-core framework\n" + "  https://doi.org/10.1038/s41587-020-0439-x\n\n" + "* Software dependencies\n" + "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
 }
 
 //
@@ -102,7 +94,7 @@ def getWorkflowVersion() {
 //
 def processVersionsFromYAML(yaml_file) {
     def yaml = new org.yaml.snakeyaml.Yaml()
-    def versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] }
+    def versions = yaml.load(yaml_file).collectEntries { k, v -> [k.tokenize(':')[-1], v] }
     return yaml.dumpAsMap(versions).trim()
 }
 
@@ -112,8 +104,8 @@ def processVersionsFromYAML(yaml_file) {
 def workflowVersionToYAML() {
     return """
     Workflow:
-        $workflow.manifest.name: ${getWorkflowVersion()}
-        Nextflow: $workflow.nextflow.version
+        ${workflow.manifest.name}: ${getWorkflowVersion()}
+        Nextflow: ${workflow.nextflow.version}
     """.stripIndent().trim()
 }
 
@@ -121,11 +113,7 @@ def workflowVersionToYAML() {
 // Get channel of software versions used in pipeline in YAML format
 //
 def softwareVersionsToYAML(ch_versions) {
-    return ch_versions
-                .unique()
-                .map { version -> processVersionsFromYAML(version) }
-                .unique()
-                .mix(Channel.of(workflowVersionToYAML()))
+    return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML()))
 }
 
 //
@@ -133,25 +121,31 @@ def softwareVersionsToYAML(ch_versions) {
 //
 def paramsSummaryMultiqc(summary_params) {
     def summary_section = ''
-    summary_params.keySet().each { group ->
-        def group_params = summary_params.get(group)  // This gets the parameters of that particular group
-        if (group_params) {
-            summary_section += "    <p style=\"font-size:110%\"><b>$group</b></p>\n"
-            summary_section += "    <dl class=\"dl-horizontal\">\n"
-            group_params.keySet().sort().each { param ->
-                summary_section += "        <dt>$param</dt><dd><samp>${group_params.get(param) ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>\n"
+    summary_params
+        .keySet()
+        .each { group ->
+            def group_params = summary_params.get(group)
+            // This gets the parameters of that particular group
+            if (group_params) {
+                summary_section += "    <p style=\"font-size:110%\"><b>${group}</b></p>\n"
+                summary_section += "    <dl class=\"dl-horizontal\">\n"
+                group_params
+                    .keySet()
+                    .sort()
+                    .each { param ->
+                        summary_section += "        <dt>${param}</dt><dd><samp>${group_params.get(param) ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>\n"
+                    }
+                summary_section += "    </dl>\n"
             }
-            summary_section += "    </dl>\n"
         }
-    }
 
-    def yaml_file_text  = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" as String
-    yaml_file_text        += "description: ' - this information is collected when the pipeline is started.'\n"
-    yaml_file_text        += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
-    yaml_file_text        += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
-    yaml_file_text        += "plot_type: 'html'\n"
-    yaml_file_text        += "data: |\n"
-    yaml_file_text        += "${summary_section}"
+    def yaml_file_text = "id: '${workflow.manifest.name.replace('/', '-')}-summary'\n" as String
+    yaml_file_text     += "description: ' - this information is collected when the pipeline is started.'\n"
+    yaml_file_text     += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
+    yaml_file_text     += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
+    yaml_file_text     += "plot_type: 'html'\n"
+    yaml_file_text     += "data: |\n"
+    yaml_file_text     += "${summary_section}"
 
     return yaml_file_text
 }
@@ -199,54 +193,54 @@ def logColours(monochrome_logs=true) {
     colorcodes['hidden']     = monochrome_logs ? '' : "\033[8m"
 
     // Regular Colors
-    colorcodes['black']      = monochrome_logs ? '' : "\033[0;30m"
-    colorcodes['red']        = monochrome_logs ? '' : "\033[0;31m"
-    colorcodes['green']      = monochrome_logs ? '' : "\033[0;32m"
-    colorcodes['yellow']     = monochrome_logs ? '' : "\033[0;33m"
-    colorcodes['blue']       = monochrome_logs ? '' : "\033[0;34m"
-    colorcodes['purple']     = monochrome_logs ? '' : "\033[0;35m"
-    colorcodes['cyan']       = monochrome_logs ? '' : "\033[0;36m"
-    colorcodes['white']      = monochrome_logs ? '' : "\033[0;37m"
+    colorcodes['black']  = monochrome_logs ? '' : "\033[0;30m"
+    colorcodes['red']    = monochrome_logs ? '' : "\033[0;31m"
+    colorcodes['green']  = monochrome_logs ? '' : "\033[0;32m"
+    colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m"
+    colorcodes['blue']   = monochrome_logs ? '' : "\033[0;34m"
+    colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m"
+    colorcodes['cyan']   = monochrome_logs ? '' : "\033[0;36m"
+    colorcodes['white']  = monochrome_logs ? '' : "\033[0;37m"
 
     // Bold
-    colorcodes['bblack']     = monochrome_logs ? '' : "\033[1;30m"
-    colorcodes['bred']       = monochrome_logs ? '' : "\033[1;31m"
-    colorcodes['bgreen']     = monochrome_logs ? '' : "\033[1;32m"
-    colorcodes['byellow']    = monochrome_logs ? '' : "\033[1;33m"
-    colorcodes['bblue']      = monochrome_logs ? '' : "\033[1;34m"
-    colorcodes['bpurple']    = monochrome_logs ? '' : "\033[1;35m"
-    colorcodes['bcyan']      = monochrome_logs ? '' : "\033[1;36m"
-    colorcodes['bwhite']     = monochrome_logs ? '' : "\033[1;37m"
+    colorcodes['bblack']  = monochrome_logs ? '' : "\033[1;30m"
+    colorcodes['bred']    = monochrome_logs ? '' : "\033[1;31m"
+    colorcodes['bgreen']  = monochrome_logs ? '' : "\033[1;32m"
+    colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m"
+    colorcodes['bblue']   = monochrome_logs ? '' : "\033[1;34m"
+    colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m"
+    colorcodes['bcyan']   = monochrome_logs ? '' : "\033[1;36m"
+    colorcodes['bwhite']  = monochrome_logs ? '' : "\033[1;37m"
 
     // Underline
-    colorcodes['ublack']     = monochrome_logs ? '' : "\033[4;30m"
-    colorcodes['ured']       = monochrome_logs ? '' : "\033[4;31m"
-    colorcodes['ugreen']     = monochrome_logs ? '' : "\033[4;32m"
-    colorcodes['uyellow']    = monochrome_logs ? '' : "\033[4;33m"
-    colorcodes['ublue']      = monochrome_logs ? '' : "\033[4;34m"
-    colorcodes['upurple']    = monochrome_logs ? '' : "\033[4;35m"
-    colorcodes['ucyan']      = monochrome_logs ? '' : "\033[4;36m"
-    colorcodes['uwhite']     = monochrome_logs ? '' : "\033[4;37m"
+    colorcodes['ublack']  = monochrome_logs ? '' : "\033[4;30m"
+    colorcodes['ured']    = monochrome_logs ? '' : "\033[4;31m"
+    colorcodes['ugreen']  = monochrome_logs ? '' : "\033[4;32m"
+    colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m"
+    colorcodes['ublue']   = monochrome_logs ? '' : "\033[4;34m"
+    colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m"
+    colorcodes['ucyan']   = monochrome_logs ? '' : "\033[4;36m"
+    colorcodes['uwhite']  = monochrome_logs ? '' : "\033[4;37m"
 
     // High Intensity
-    colorcodes['iblack']     = monochrome_logs ? '' : "\033[0;90m"
-    colorcodes['ired']       = monochrome_logs ? '' : "\033[0;91m"
-    colorcodes['igreen']     = monochrome_logs ? '' : "\033[0;92m"
-    colorcodes['iyellow']    = monochrome_logs ? '' : "\033[0;93m"
-    colorcodes['iblue']      = monochrome_logs ? '' : "\033[0;94m"
-    colorcodes['ipurple']    = monochrome_logs ? '' : "\033[0;95m"
-    colorcodes['icyan']      = monochrome_logs ? '' : "\033[0;96m"
-    colorcodes['iwhite']     = monochrome_logs ? '' : "\033[0;97m"
+    colorcodes['iblack']  = monochrome_logs ? '' : "\033[0;90m"
+    colorcodes['ired']    = monochrome_logs ? '' : "\033[0;91m"
+    colorcodes['igreen']  = monochrome_logs ? '' : "\033[0;92m"
+    colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m"
+    colorcodes['iblue']   = monochrome_logs ? '' : "\033[0;94m"
+    colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m"
+    colorcodes['icyan']   = monochrome_logs ? '' : "\033[0;96m"
+    colorcodes['iwhite']  = monochrome_logs ? '' : "\033[0;97m"
 
     // Bold High Intensity
-    colorcodes['biblack']    = monochrome_logs ? '' : "\033[1;90m"
-    colorcodes['bired']      = monochrome_logs ? '' : "\033[1;91m"
-    colorcodes['bigreen']    = monochrome_logs ? '' : "\033[1;92m"
-    colorcodes['biyellow']   = monochrome_logs ? '' : "\033[1;93m"
-    colorcodes['biblue']     = monochrome_logs ? '' : "\033[1;94m"
-    colorcodes['bipurple']   = monochrome_logs ? '' : "\033[1;95m"
-    colorcodes['bicyan']     = monochrome_logs ? '' : "\033[1;96m"
-    colorcodes['biwhite']    = monochrome_logs ? '' : "\033[1;97m"
+    colorcodes['biblack']  = monochrome_logs ? '' : "\033[1;90m"
+    colorcodes['bired']    = monochrome_logs ? '' : "\033[1;91m"
+    colorcodes['bigreen']  = monochrome_logs ? '' : "\033[1;92m"
+    colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m"
+    colorcodes['biblue']   = monochrome_logs ? '' : "\033[1;94m"
+    colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m"
+    colorcodes['bicyan']   = monochrome_logs ? '' : "\033[1;96m"
+    colorcodes['biwhite']  = monochrome_logs ? '' : "\033[1;97m"
 
     return colorcodes
 }
@@ -261,14 +255,15 @@ def attachMultiqcReport(multiqc_report) {
             mqc_report = multiqc_report.getVal()
             if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) {
                 if (mqc_report.size() > 1) {
-                    log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one"
+                    log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one")
                 }
                 mqc_report = mqc_report[0]
             }
         }
-    } catch (all) {
+    }
+    catch (Exception all) {
         if (multiqc_report) {
-            log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email"
+            log.warn("[${workflow.manifest.name}] Could not attach MultiQC report to summary email")
         }
     }
     return mqc_report
@@ -280,26 +275,35 @@ def attachMultiqcReport(multiqc_report) {
 def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true, multiqc_report=null) {
 
     // Set up the e-mail variables
-    def subject = "[$workflow.manifest.name] Successful: $workflow.runName"
+    def subject = "[${workflow.manifest.name}] Successful: ${workflow.runName}"
     if (!workflow.success) {
-        subject = "[$workflow.manifest.name] FAILED: $workflow.runName"
+        subject = "[${workflow.manifest.name}] FAILED: ${workflow.runName}"
     }
 
     def summary = [:]
-    summary_params.keySet().sort().each { group ->
-        summary << summary_params[group]
-    }
+    summary_params
+        .keySet()
+        .sort()
+        .each { group ->
+            summary << summary_params[group]
+        }
 
     def misc_fields = [:]
     misc_fields['Date Started']              = workflow.start
     misc_fields['Date Completed']            = workflow.complete
     misc_fields['Pipeline script file path'] = workflow.scriptFile
     misc_fields['Pipeline script hash ID']   = workflow.scriptId
-    if (workflow.repository) misc_fields['Pipeline repository Git URL']    = workflow.repository
-    if (workflow.commitId)   misc_fields['Pipeline repository Git Commit'] = workflow.commitId
-    if (workflow.revision)   misc_fields['Pipeline Git branch/tag']        = workflow.revision
-    misc_fields['Nextflow Version']           = workflow.nextflow.version
-    misc_fields['Nextflow Build']             = workflow.nextflow.build
+    if (workflow.repository) {
+        misc_fields['Pipeline repository Git URL']    = workflow.repository
+    }
+    if (workflow.commitId) {
+        misc_fields['Pipeline repository Git Commit'] = workflow.commitId
+    }
+    if (workflow.revision) {
+        misc_fields['Pipeline Git branch/tag']        = workflow.revision
+    }
+    misc_fields['Nextflow Version']          = workflow.nextflow.version
+    misc_fields['Nextflow Build']            = workflow.nextflow.build
     misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
 
     def email_fields = [:]
@@ -337,7 +341,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
 
     // Render the sendmail template
     def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit
-    def smail_fields           = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ]
+    def smail_fields           = [email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes()]
     def sf                     = new File("${workflow.projectDir}/assets/sendmail_template.txt")
     def sendmail_template      = engine.createTemplate(sf).make(smail_fields)
     def sendmail_html          = sendmail_template.toString()
@@ -346,30 +350,32 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     def colors = logColours(monochrome_logs) as Map
     if (email_address) {
         try {
-            if (plaintext_email) { throw new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') }
+            if (plaintext_email) {
+new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML')            }
             // Try to send HTML e-mail using sendmail
             def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html")
             sendmail_tf.withWriter { w -> w << sendmail_html }
-            [ 'sendmail', '-t' ].execute() << sendmail_html
-            log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-"
-        } catch (all) {
+            ['sendmail', '-t'].execute() << sendmail_html
+            log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (sendmail)-")
+        }
+        catch (Exception all) {
             // Catch failures and try with plaintext
-            def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ]
+            def mail_cmd = ['mail', '-s', subject, '--content-type=text/html', email_address]
             mail_cmd.execute() << email_html
-            log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-"
+            log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (mail)-")
         }
     }
 
     // Write summary e-mail HTML to a file
     def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html")
     output_hf.withWriter { w -> w << email_html }
-    nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html");
+    nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html")
     output_hf.delete()
 
     // Write summary e-mail TXT to a file
     def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt")
     output_tf.withWriter { w -> w << email_txt }
-    nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt");
+    nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt")
     output_tf.delete()
 }
 
@@ -380,12 +386,14 @@ def completionSummary(monochrome_logs=true) {
     def colors = logColours(monochrome_logs) as Map
     if (workflow.success) {
         if (workflow.stats.ignoredCount == 0) {
-            log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-"
-        } else {
-            log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-"
+            log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Pipeline completed successfully${colors.reset}-")
+        }
+        else {
+            log.info("-${colors.purple}[${workflow.manifest.name}]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-")
         }
-    } else {
-        log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-"
+    }
+    else {
+        log.info("-${colors.purple}[${workflow.manifest.name}]${colors.red} Pipeline completed with errors${colors.reset}-")
     }
 }
 
@@ -394,21 +402,30 @@ def completionSummary(monochrome_logs=true) {
 //
 def imNotification(summary_params, hook_url) {
     def summary = [:]
-    summary_params.keySet().sort().each { group ->
-        summary << summary_params[group]
-    }
+    summary_params
+        .keySet()
+        .sort()
+        .each { group ->
+            summary << summary_params[group]
+        }
 
     def misc_fields = [:]
-    misc_fields['start']                                = workflow.start
-    misc_fields['complete']                             = workflow.complete
-    misc_fields['scriptfile']                           = workflow.scriptFile
-    misc_fields['scriptid']                             = workflow.scriptId
-    if (workflow.repository) misc_fields['repository']  = workflow.repository
-    if (workflow.commitId)   misc_fields['commitid']    = workflow.commitId
-    if (workflow.revision)   misc_fields['revision']    = workflow.revision
-    misc_fields['nxf_version']                          = workflow.nextflow.version
-    misc_fields['nxf_build']                            = workflow.nextflow.build
-    misc_fields['nxf_timestamp']                        = workflow.nextflow.timestamp
+    misc_fields['start']          = workflow.start
+    misc_fields['complete']       = workflow.complete
+    misc_fields['scriptfile']     = workflow.scriptFile
+    misc_fields['scriptid']       = workflow.scriptId
+    if (workflow.repository) {
+        misc_fields['repository'] = workflow.repository
+    }
+    if (workflow.commitId) {
+        misc_fields['commitid']   = workflow.commitId
+    }
+    if (workflow.revision) {
+        misc_fields['revision']   = workflow.revision
+    }
+    misc_fields['nxf_version']    = workflow.nextflow.version
+    misc_fields['nxf_build']      = workflow.nextflow.build
+    misc_fields['nxf_timestamp']  = workflow.nextflow.timestamp
 
     def msg_fields = [:]
     msg_fields['version']      = getWorkflowVersion()
@@ -433,13 +450,13 @@ def imNotification(summary_params, hook_url) {
     def json_message  = json_template.toString()
 
     // POST
-    def post = new URL(hook_url).openConnection();
+    def post = new URL(hook_url).openConnection()
     post.setRequestMethod("POST")
     post.setDoOutput(true)
     post.setRequestProperty("Content-Type", "application/json")
-    post.getOutputStream().write(json_message.getBytes("UTF-8"));
-    def postRC = post.getResponseCode();
-    if (! postRC.equals(200)) {
-        log.warn(post.getErrorStream().getText());
+    post.getOutputStream().write(json_message.getBytes("UTF-8"))
+    def postRC = post.getResponseCode()
+    if (!postRC.equals(200)) {
+        log.warn(post.getErrorStream().getText())
     }
 }

From 7566c9fb5396391f4a321806484ece1c1fd627f1 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Fri, 11 Oct 2024 12:35:06 +0000
Subject: [PATCH 53/58] Template update for nf-core/tools version 3.0.2

---
 .github/workflows/ci.yml                      | 60 +++++++++++++------
 .../workflows/template_version_comment.yml    | 21 ++++---
 .gitignore                                    |  1 +
 .nf-core.yml                                  |  2 +-
 main.nf                                       |  2 +-
 modules.json                                  |  6 +-
 modules/nf-core/multiqc/main.nf               |  2 +-
 nextflow.config                               |  4 +-
 .../main.nf                                   |  4 +-
 .../nf-core/utils_nextflow_pipeline/main.nf   | 30 +++++-----
 .../nf-core/utils_nfcore_pipeline/main.nf     | 10 ++--
 workflows/seqinspector.nf                     |  2 -
 12 files changed, 86 insertions(+), 58 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 5666673..81d0308 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -11,6 +11,8 @@ on:
 
 env:
   NXF_ANSI_LOG: false
+  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
+  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
 
 concurrency:
   group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
@@ -18,7 +20,7 @@ concurrency:
 
 jobs:
   test:
-    name: Run pipeline with test data
+    name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})"
     # Only run on push if this is the nf-core dev branch (merged PRs)
     if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/seqinspector') }}"
     runs-on: ubuntu-latest
@@ -27,33 +29,57 @@ jobs:
         NXF_VER:
           - "24.04.2"
           - "latest-everything"
+        profile:
+          - "conda"
+          - "docker"
+          - "singularity"
+        test_name:
+          - "test"
+        isMaster:
+          - ${{ github.base_ref == 'master' }}
+        # Exclude conda and singularity on dev
+        exclude:
+          - isMaster: false
+            profile: "conda"
+          - isMaster: false
+            profile: "singularity"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
-      - name: Install Nextflow
+      - name: Set up Nextflow
         uses: nf-core/setup-nextflow@v2
         with:
           version: "${{ matrix.NXF_VER }}"
 
-      - name: Disk space cleanup
-        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+      - name: Set up Apptainer
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-apptainer@main
 
-      - name: Run pipeline with test data (docker)
-        # TODO nf-core: You can customise CI pipeline run tests as required
-        # For example: adding multiple test runs with different parameters
-        # Remember that you can parallelise this by using strategy.matrix
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
+          mkdir -p $NXF_SINGULARITY_CACHEDIR
+          mkdir -p $NXF_SINGULARITY_LIBRARYDIR
+
+      - name: Set up Miniconda
+        if: matrix.profile == 'conda'
+        uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3
+        with:
+          miniconda-version: "latest"
+          auto-update-conda: true
+          conda-solver: libmamba
+          channels: conda-forge,bioconda
 
-      - name: Run pipeline with test data (singularity)
-        # TODO nf-core: You can customise CI pipeline run tests as required
+      - name: Set up Conda
+        if: matrix.profile == 'conda'
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,singularity --outdir ./results
-        if: "${{ github.base_ref == 'master' }}"
+          echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
+          echo $(realpath python) >> $GITHUB_PATH
+
+      - name: Clean up Disk space
+        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - name: Run pipeline with test data (conda)
-        # TODO nf-core: You can customise CI pipeline run tests as required
+      - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,conda --outdir ./results
-        if: "${{ github.base_ref == 'master' }}"
+          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results
diff --git a/.github/workflows/template_version_comment.yml b/.github/workflows/template_version_comment.yml
index 9dea41f..e8aafe4 100644
--- a/.github/workflows/template_version_comment.yml
+++ b/.github/workflows/template_version_comment.yml
@@ -10,9 +10,11 @@ jobs:
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        with:
+          ref: ${{ github.event.pull_request.head.sha }}
 
       - name: Read template version from .nf-core.yml
-        uses: pietrobolcato/action-read-yaml@1.0.0
+        uses: nichmor/minimal-read-yaml@v0.0.2
         id: read_yml
         with:
           config: ${{ github.workspace }}/.nf-core.yml
@@ -24,20 +26,21 @@ jobs:
 
       - name: Check nf-core outdated
         id: nf_core_outdated
-        run: pip list --outdated | grep nf-core
+        run: echo "OUTPUT=$(pip list --outdated | grep nf-core)" >> ${GITHUB_ENV}
 
       - name: Post nf-core template version comment
         uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
         if: |
-          ${{ steps.nf_core_outdated.outputs.stdout }} =~ 'nf-core'
+          contains(env.OUTPUT, 'nf-core')
         with:
           repo-token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }}
           allow-repeats: false
           message: |
-            ## :warning: Newer version of the nf-core template is available.
-
-            Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}.
-            Please update your pipeline to the latest version.
-
-            For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync).
+            > [!WARNING]
+            > Newer version of the nf-core template is available.
+            >
+            > Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}.
+            > Please update your pipeline to the latest version.
+            >
+            > For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync).
           #
diff --git a/.gitignore b/.gitignore
index 5124c9a..a42ce01 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,3 +6,4 @@ results/
 testing/
 testing*
 *.pyc
+null/
diff --git a/.nf-core.yml b/.nf-core.yml
index 4e85672..fb85600 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,6 +1,6 @@
 bump_version: null
 lint: null
-nf_core_version: 3.0.1
+nf_core_version: 3.0.2
 org_path: null
 repository_type: pipeline
 template:
diff --git a/main.nf b/main.nf
index df5d216..58e593b 100644
--- a/main.nf
+++ b/main.nf
@@ -76,7 +76,7 @@ workflow {
         params.outdir,
         params.input
     )
-    
+
     //
     // WORKFLOW: Run main workflow
     //
diff --git a/modules.json b/modules.json
index 4178960..8e632d5 100644
--- a/modules.json
+++ b/modules.json
@@ -12,7 +12,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "b8d36829fa84b6e404364abff787e8b07f6d058c",
+                        "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
                         "installed_by": ["modules"]
                     }
                 }
@@ -21,12 +21,12 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "9d05360da397692321d377b6102d2fb22507c6ef",
+                        "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "772684d9d66f37b650c8ba5146ac1ee3ecba2acb",
+                        "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index 9724d2f..cc0643e 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -52,7 +52,7 @@ process MULTIQC {
     stub:
     """
     mkdir multiqc_data
-    touch multiqc_plots
+    mkdir multiqc_plots
     touch multiqc_report.html
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/nextflow.config b/nextflow.config
index caea85a..1c1ca6b 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -254,10 +254,10 @@ validation {
 """
         afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "  https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
 * The nf-core framework
-  https://doi.org/10.1038/s41587-020-0439-x
+    https://doi.org/10.1038/s41587-020-0439-x
 
 * Software dependencies
-  https://github.com/${manifest.name}/blob/master/CITATIONS.md
+    https://github.com/${manifest.name}/blob/master/CITATIONS.md
 """
     }
     summary {
diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index b255821..8384b83 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -47,7 +47,6 @@ workflow PIPELINE_INITIALISATION {
         workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1
     )
 
-    
     //
     // Validate parameters and generate parameter summary to stdout
     //
@@ -56,7 +55,6 @@ workflow PIPELINE_INITIALISATION {
         validate_params,
         null
     )
-    
 
     //
     // Check config provided to the pipeline
@@ -64,6 +62,7 @@ workflow PIPELINE_INITIALISATION {
     UTILS_NFCORE_PIPELINE (
         nextflow_cli_args
     )
+
     //
     // Custom validation for pipeline parameters
     //
@@ -110,7 +109,6 @@ workflow PIPELINE_COMPLETION {
     email           //  string: email address
     email_on_fail   //  string: email address sent on pipeline failure
     plaintext_email // boolean: Send plain-text email instead of HTML
-    
     outdir          //    path: Path to output directory where results will be published
     monochrome_logs // boolean: Disable ANSI colour codes in log output
     hook_url        //  string: hook URL for notifications
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
index 2b0dc67..0fcbf7b 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
@@ -3,9 +3,9 @@
 //
 
 /*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUBWORKFLOW DEFINITION
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow UTILS_NEXTFLOW_PIPELINE {
@@ -44,9 +44,9 @@ workflow UTILS_NEXTFLOW_PIPELINE {
 }
 
 /*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     FUNCTIONS
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 //
@@ -106,17 +106,19 @@ def checkCondaChannels() {
     def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean
 
     // Check that they are in the right order
-    def channel_priority_violation = false
-
-    required_channels_in_order.eachWithIndex { channel, index ->
-        if (index < required_channels_in_order.size() - 1) {
-            channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index + 1]))
-        }
-    }
+    def channel_priority_violation = required_channels_in_order != channels.findAll { ch -> ch in required_channels_in_order }
 
     if (channels_missing | channel_priority_violation) {
-        log.warn(
-            "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + "  There is a problem with your Conda configuration!\n\n" + "  You will need to set-up the conda-forge and bioconda channels correctly.\n" + "  Please refer to https://bioconda.github.io/\n" + "  The observed channel order is \n" + "  ${channels}\n" + "  but the following channel order is required:\n" + "  ${required_channels_in_order}\n" + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-        )
+        log.warn """\
+        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+            There is a problem with your Conda configuration!
+            You will need to set-up the conda-forge and bioconda channels correctly.
+            Please refer to https://bioconda.github.io/
+            The observed channel order is
+            ${channels}
+            but the following channel order is required:
+            ${required_channels_in_order}
+        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+        """.stripIndent(true)
     }
 }
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index b78273c..5cb7baf 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -3,9 +3,9 @@
 //
 
 /*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUBWORKFLOW DEFINITION
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow UTILS_NFCORE_PIPELINE {
@@ -21,9 +21,9 @@ workflow UTILS_NFCORE_PIPELINE {
 }
 
 /*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     FUNCTIONS
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 //
@@ -62,7 +62,7 @@ def checkProfileProvided(nextflow_cli_args) {
 def workflowCitation() {
     def temp_doi_ref = ""
     def manifest_doi = workflow.manifest.doi.tokenize(",")
-    // Using a loop to handle multiple DOIs
+    // Handling multiple DOIs
     // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
     // Removing ` ` since the manifest.doi is a string and not a proper list
     manifest_doi.each { doi_ref ->
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index af3719c..4a9df1c 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -57,13 +57,11 @@ workflow SEQINSPECTOR {
         Channel.fromPath(params.multiqc_logo, checkIfExists: true) :
         Channel.empty()
 
-    
     summary_params      = paramsSummaryMap(
         workflow, parameters_schema: "nextflow_schema.json")
     ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
     ch_multiqc_files = ch_multiqc_files.mix(
         ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
-    
     ch_multiqc_custom_methods_description = params.multiqc_methods_description ?
         file(params.multiqc_methods_description, checkIfExists: true) :
         file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)

From 7ce086a6fddbe96de440a234128576bfc4d6bff5 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Mon, 28 Oct 2024 11:12:03 +0000
Subject: [PATCH 54/58] nf-core tools 3.0.2 modules update

---
 modules.json                                  |   4 +-
 modules/nf-core/fastqc/environment.yml        |   2 -
 modules/nf-core/fastqc/main.nf                |   5 +-
 modules/nf-core/fastqc/meta.yml               |  57 +--
 modules/nf-core/fastqc/tests/main.nf.test     | 225 ++++++++---
 .../nf-core/fastqc/tests/main.nf.test.snap    | 370 ++++++++++++++++--
 modules/nf-core/multiqc/environment.yml       |   4 +-
 modules/nf-core/multiqc/main.nf               |   6 +-
 modules/nf-core/multiqc/meta.yml              |  91 +++--
 .../nf-core/multiqc/tests/main.nf.test.snap   |  26 +-
 10 files changed, 603 insertions(+), 187 deletions(-)

diff --git a/modules.json b/modules.json
index 70f3486..a84d111 100644
--- a/modules.json
+++ b/modules.json
@@ -7,12 +7,12 @@
                 "nf-core": {
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "19ca321db5d8bd48923262c2eca6422359633491",
+                        "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
                         "installed_by": ["modules"]
                     }
                 }
diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml
index 1787b38..691d4c7 100644
--- a/modules/nf-core/fastqc/environment.yml
+++ b/modules/nf-core/fastqc/environment.yml
@@ -1,7 +1,5 @@
-name: fastqc
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::fastqc=0.12.1
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index d79f1c8..d8989f4 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -26,7 +26,10 @@ process FASTQC {
     def rename_to = old_new_pairs*.join(' ').join(' ')
     def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
 
-    def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB')
+    // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory)
+    // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222
+    // Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label
+    def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') / task.cpus
     // FastQC memory value allowed range (100 - 10000)
     def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb)
 
diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml
index ee5507e..4827da7 100644
--- a/modules/nf-core/fastqc/meta.yml
+++ b/modules/nf-core/fastqc/meta.yml
@@ -16,35 +16,44 @@ tools:
       homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
       documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
       licence: ["GPL-2.0-only"]
+      identifier: biotools:fastqc
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - reads:
-      type: file
-      description: |
-        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
-        respectively.
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - reads:
+        type: file
+        description: |
+          List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+          respectively.
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
   - html:
-      type: file
-      description: FastQC report
-      pattern: "*_{fastqc.html}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.html":
+          type: file
+          description: FastQC report
+          pattern: "*_{fastqc.html}"
   - zip:
-      type: file
-      description: FastQC report archive
-      pattern: "*_{fastqc.zip}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.zip":
+          type: file
+          description: FastQC report archive
+          pattern: "*_{fastqc.zip}"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@drpatelh"
   - "@grst"
diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test
index 70edae4..e9d79a0 100644
--- a/modules/nf-core/fastqc/tests/main.nf.test
+++ b/modules/nf-core/fastqc/tests/main.nf.test
@@ -23,17 +23,14 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-
-            // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it.
-            // looks like this: <div id="header_filename">Mon 2 Oct 2023<br/>test.gz</div>
-            // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039
-
-            { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
-            { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
-            { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-
-            { assert snapshot(process.out.versions).match("fastqc_versions_single") }
+                { assert process.success },
+                // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it.
+                // looks like this: <div id="header_filename">Mon 2 Oct 2023<br/>test.gz</div>
+                // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039
+                { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
+                { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
+                { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert snapshot(process.out.versions).match() }
             )
         }
     }
@@ -54,16 +51,14 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-
-            { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
-            { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
-            { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
-            { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
-            { assert path(process.out.html[0][1][0]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-            { assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-
-            { assert snapshot(process.out.versions).match("fastqc_versions_paired") }
+                { assert process.success },
+                { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
+                { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
+                { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
+                { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
+                { assert path(process.out.html[0][1][0]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert snapshot(process.out.versions).match() }
             )
         }
     }
@@ -83,13 +78,11 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-
-            { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
-            { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
-            { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-
-            { assert snapshot(process.out.versions).match("fastqc_versions_interleaved") }
+                { assert process.success },
+                { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
+                { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
+                { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert snapshot(process.out.versions).match() }
             )
         }
     }
@@ -109,13 +102,11 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-
-            { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
-            { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
-            { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-
-            { assert snapshot(process.out.versions).match("fastqc_versions_bam") }
+                { assert process.success },
+                { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
+                { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
+                { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert snapshot(process.out.versions).match() }
             )
         }
     }
@@ -138,22 +129,20 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-
-            { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
-            { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
-            { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" },
-            { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" },
-            { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
-            { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
-            { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" },
-            { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" },
-            { assert path(process.out.html[0][1][0]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-            { assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-            { assert path(process.out.html[0][1][2]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-            { assert path(process.out.html[0][1][3]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-
-            { assert snapshot(process.out.versions).match("fastqc_versions_multiple") }
+                { assert process.success },
+                { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
+                { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
+                { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" },
+                { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" },
+                { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
+                { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
+                { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" },
+                { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" },
+                { assert path(process.out.html[0][1][0]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert path(process.out.html[0][1][2]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert path(process.out.html[0][1][3]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert snapshot(process.out.versions).match() }
             )
         }
     }
@@ -173,21 +162,18 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-
-            { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" },
-            { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" },
-            { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-
-            { assert snapshot(process.out.versions).match("fastqc_versions_custom_prefix") }
+                { assert process.success },
+                { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" },
+                { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" },
+                { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert snapshot(process.out.versions).match() }
             )
         }
     }
 
     test("sarscov2 single-end [fastq] - stub") {
 
-        options "-stub"
-
+    options "-stub"
         when {
             process {
                 """
@@ -201,12 +187,123 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-            { assert snapshot(process.out.html.collect { file(it[1]).getName() } +
-                                process.out.zip.collect { file(it[1]).getName() } +
-                                process.out.versions ).match("fastqc_stub") }
+                { assert process.success },
+                { assert snapshot(process.out).match() }
             )
         }
     }
 
+    test("sarscov2 paired-end [fastq] - stub") {
+
+    options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 interleaved [fastq] - stub") {
+
+    options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true)
+                ])
+            """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 paired-end [bam] - stub") {
+
+    options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 multiple [fastq] - stub") {
+
+    options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 custom_prefix - stub") {
+
+    options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'mysample', single_end:true ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
 }
diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap
index 86f7c31..d5db309 100644
--- a/modules/nf-core/fastqc/tests/main.nf.test.snap
+++ b/modules/nf-core/fastqc/tests/main.nf.test.snap
@@ -1,88 +1,392 @@
 {
-    "fastqc_versions_interleaved": {
+    "sarscov2 custom_prefix": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:40:07.293713"
+        "timestamp": "2024-07-22T11:02:16.374038"
     },
-    "fastqc_stub": {
+    "sarscov2 single-end [fastq] - stub": {
         "content": [
-            [
-                "test.html",
-                "test.zip",
-                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
-            ]
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:02:24.993809"
+    },
+    "sarscov2 custom_prefix - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "mysample",
+                            "single_end": true
+                        },
+                        "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "mysample",
+                            "single_end": true
+                        },
+                        "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "mysample",
+                            "single_end": true
+                        },
+                        "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "mysample",
+                            "single_end": true
+                        },
+                        "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:31:01.425198"
+        "timestamp": "2024-07-22T11:03:10.93942"
     },
-    "fastqc_versions_multiple": {
+    "sarscov2 interleaved [fastq]": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:40:55.797907"
+        "timestamp": "2024-07-22T11:01:42.355718"
     },
-    "fastqc_versions_bam": {
+    "sarscov2 paired-end [bam]": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:40:26.795862"
+        "timestamp": "2024-07-22T11:01:53.276274"
     },
-    "fastqc_versions_single": {
+    "sarscov2 multiple [fastq]": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:39:27.043675"
+        "timestamp": "2024-07-22T11:02:05.527626"
     },
-    "fastqc_versions_paired": {
+    "sarscov2 paired-end [fastq]": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:01:31.188871"
+    },
+    "sarscov2 paired-end [fastq] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:02:34.273566"
+    },
+    "sarscov2 multiple [fastq] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:39:47.584191"
+        "timestamp": "2024-07-22T11:03:02.304411"
     },
-    "fastqc_versions_custom_prefix": {
+    "sarscov2 single-end [fastq]": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:01:19.095607"
+    },
+    "sarscov2 interleaved [fastq] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:02:44.640184"
+    },
+    "sarscov2 paired-end [bam] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:41:14.576531"
+        "timestamp": "2024-07-22T11:02:53.550742"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index a31464c..6f5b867 100644
--- a/modules/nf-core/multiqc/environment.yml
+++ b/modules/nf-core/multiqc/environment.yml
@@ -1,7 +1,5 @@
-name: multiqc
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - bioconda::multiqc=1.24.1
+  - bioconda::multiqc=1.25.1
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index ceaec13..cc0643e 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -3,8 +3,8 @@ process MULTIQC {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.24.1--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.24.1--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.25.1--pyhdfd78af_0' }"
 
     input:
     path  multiqc_files, stageAs: "?/*"
@@ -52,7 +52,7 @@ process MULTIQC {
     stub:
     """
     mkdir multiqc_data
-    touch multiqc_plots
+    mkdir multiqc_plots
     touch multiqc_report.html
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
index 382c08c..b16c187 100644
--- a/modules/nf-core/multiqc/meta.yml
+++ b/modules/nf-core/multiqc/meta.yml
@@ -1,5 +1,6 @@
 name: multiqc
-description: Aggregate results from bioinformatics analyses across many samples into a single report
+description: Aggregate results from bioinformatics analyses across many samples into
+  a single report
 keywords:
   - QC
   - bioinformatics tools
@@ -12,53 +13,59 @@ tools:
       homepage: https://multiqc.info/
       documentation: https://multiqc.info/docs/
       licence: ["GPL-3.0-or-later"]
+      identifier: biotools:multiqc
 input:
-  - multiqc_files:
-      type: file
-      description: |
-        List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
-  - multiqc_config:
-      type: file
-      description: Optional config yml for MultiQC
-      pattern: "*.{yml,yaml}"
-  - extra_multiqc_config:
-      type: file
-      description: Second optional config yml for MultiQC. Will override common sections in multiqc_config.
-      pattern: "*.{yml,yaml}"
-  - multiqc_logo:
-      type: file
-      description: Optional logo file for MultiQC
-      pattern: "*.{png}"
-  - replace_names:
-      type: file
-      description: |
-        Optional two-column sample renaming file. First column a set of
-        patterns, second column a set of corresponding replacements. Passed via
-        MultiQC's `--replace-names` option.
-      pattern: "*.{tsv}"
-  - sample_names:
-      type: file
-      description: |
-        Optional TSV file with headers, passed to the MultiQC --sample_names
-        argument.
-      pattern: "*.{tsv}"
+  - - multiqc_files:
+        type: file
+        description: |
+          List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
+  - - multiqc_config:
+        type: file
+        description: Optional config yml for MultiQC
+        pattern: "*.{yml,yaml}"
+  - - extra_multiqc_config:
+        type: file
+        description: Second optional config yml for MultiQC. Will override common sections
+          in multiqc_config.
+        pattern: "*.{yml,yaml}"
+  - - multiqc_logo:
+        type: file
+        description: Optional logo file for MultiQC
+        pattern: "*.{png}"
+  - - replace_names:
+        type: file
+        description: |
+          Optional two-column sample renaming file. First column a set of
+          patterns, second column a set of corresponding replacements. Passed via
+          MultiQC's `--replace-names` option.
+        pattern: "*.{tsv}"
+  - - sample_names:
+        type: file
+        description: |
+          Optional TSV file with headers, passed to the MultiQC --sample_names
+          argument.
+        pattern: "*.{tsv}"
 output:
   - report:
-      type: file
-      description: MultiQC report file
-      pattern: "multiqc_report.html"
+      - "*multiqc_report.html":
+          type: file
+          description: MultiQC report file
+          pattern: "multiqc_report.html"
   - data:
-      type: directory
-      description: MultiQC data dir
-      pattern: "multiqc_data"
+      - "*_data":
+          type: directory
+          description: MultiQC data dir
+          pattern: "multiqc_data"
   - plots:
-      type: file
-      description: Plots created by MultiQC
-      pattern: "*_data"
+      - "*_plots":
+          type: file
+          description: Plots created by MultiQC
+          pattern: "*_data"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@abhi18av"
   - "@bunop"
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
index 83fa080..2fcbb5f 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -2,14 +2,14 @@
     "multiqc_versions_single": {
         "content": [
             [
-                "versions.yml:md5,6eb13f3b11bbcbfc98ad3166420ff760"
+                "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-10T12:41:34.562023"
+        "timestamp": "2024-10-02T17:51:46.317523"
     },
     "multiqc_stub": {
         "content": [
@@ -17,25 +17,25 @@
                 "multiqc_report.html",
                 "multiqc_data",
                 "multiqc_plots",
-                "versions.yml:md5,6eb13f3b11bbcbfc98ad3166420ff760"
+                "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-10T11:27:11.933869532"
+        "timestamp": "2024-10-02T17:52:20.680978"
     },
     "multiqc_versions_config": {
         "content": [
             [
-                "versions.yml:md5,6eb13f3b11bbcbfc98ad3166420ff760"
+                "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-10T11:26:56.709849369"
+        "timestamp": "2024-10-02T17:52:09.185842"
     }
-}
+}
\ No newline at end of file

From a5951302f2b783a4ffe9fd1d3b11474fe48d3db6 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Mon, 28 Oct 2024 13:30:37 +0000
Subject: [PATCH 55/58] merge fix

---
 .../local/utils_nfcore_seqinspector_pipeline/main.nf         | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index c227058..a84e064 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -74,6 +74,7 @@ workflow PIPELINE_INITIALISATION {
 
     Channel
         .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
+        .toList()
         .flatMap { it.withIndex().collect {  entry, idx -> entry + "${idx+1}" } }
         .map {
             meta, fastq_1, fastq_2, idx ->
@@ -94,8 +95,8 @@ workflow PIPELINE_INITIALISATION {
                 }
         }
         .groupTuple()
-        .map { samplesheet ->
-            validateInputSamplesheet(samplesheet)
+        .map {
+            validateInputSamplesheet(it) // Applies additional group validation checks that schema_input.json cannot do.
         }
         .transpose() // Replace the map below
         // .map {

From 036408867cb7b852cf1e35089d9bd4edab29bb89 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Mon, 28 Oct 2024 13:30:48 +0000
Subject: [PATCH 56/58] update snapshots

---
 tests/MiSeq.main.nf.test.snap       |  8 ++++----
 tests/NovaSeq6000.main.nf.test.snap | 24 ++++++++++++------------
 tests/PromethION.main.nf.test.snap  | 10 +++++-----
 3 files changed, 21 insertions(+), 21 deletions(-)

diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
index 9dacaf8..4613d52 100644
--- a/tests/MiSeq.main.nf.test.snap
+++ b/tests/MiSeq.main.nf.test.snap
@@ -3,13 +3,13 @@
         "content": [
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,7b1b7fd457b60404768045b148d4c0a8",
-            "multiqc_general_stats.txt:md5,962713a1473a318f2cb29bb5290c4c8e",
-            "multiqc_software_versions.txt:md5,49e3596d49ee49d967d3b6c363b486d5"
+            "multiqc_general_stats.txt:md5,5b28a83b14cb2fe88d084d08900ebdbf",
+            "multiqc_software_versions.txt:md5,a3698a2d32e8695c38d50e3d17de5fe3"
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-09-10T08:57:05.870194"
+        "timestamp": "2024-10-28T13:18:10.3675973"
     }
 }
\ No newline at end of file
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
index 3f27e5a..ee3c22b 100644
--- a/tests/NovaSeq6000.main.nf.test.snap
+++ b/tests/NovaSeq6000.main.nf.test.snap
@@ -3,29 +3,29 @@
         "content": [
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,3730f9046b20ac5c17a86db0a33f8d5d",
-            "multiqc_general_stats.txt:md5,d521de54d1e659bf7892105f7d23d4db",
-            "multiqc_software_versions.txt:md5,49e3596d49ee49d967d3b6c363b486d5",
+            "multiqc_general_stats.txt:md5,25abe0f6a35eb4a3b056fc3cf5c13732",
+            "multiqc_software_versions.txt:md5,a3698a2d32e8695c38d50e3d17de5fe3",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,8284e25ccc21041cf3b5a32eb6a51e78",
-            "multiqc_general_stats.txt:md5,d52544eb1a505c889a2f9117cf94a5fa",
-            "multiqc_software_versions.txt:md5,49e3596d49ee49d967d3b6c363b486d5",
+            "multiqc_general_stats.txt:md5,90ee35137492b80aab36ef67f72d8921",
+            "multiqc_software_versions.txt:md5,a3698a2d32e8695c38d50e3d17de5fe3",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,f38ffdc112c73af3a41ed15848a3761f",
-            "multiqc_general_stats.txt:md5,5b1190093085ef073d4bd5818c9cde79",
-            "multiqc_software_versions.txt:md5,49e3596d49ee49d967d3b6c363b486d5",
+            "multiqc_general_stats.txt:md5,d62a2fc39e674d98783d408791803148",
+            "multiqc_software_versions.txt:md5,a3698a2d32e8695c38d50e3d17de5fe3",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,7ff71ceb8ecdf086331047f8860c3347",
-            "multiqc_general_stats.txt:md5,79c1090dd8a97912893f8491641b9dc9",
-            "multiqc_software_versions.txt:md5,49e3596d49ee49d967d3b6c363b486d5",
+            "multiqc_general_stats.txt:md5,2f09b8f199ac40cf67ba50843cebd29c",
+            "multiqc_software_versions.txt:md5,a3698a2d32e8695c38d50e3d17de5fe3",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,519ff344a896ac369bba4d5c5b8be7b5",
-            "multiqc_general_stats.txt:md5,41611bd5ab9e79425c466bf976b03bdc",
-            "multiqc_software_versions.txt:md5,49e3596d49ee49d967d3b6c363b486d5"
+            "multiqc_general_stats.txt:md5,6a1c16f068d7ba3a9225a17eb570ed9a",
+            "multiqc_software_versions.txt:md5,a3698a2d32e8695c38d50e3d17de5fe3"
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-09-10T08:58:26.732622"
+        "timestamp": "2024-10-28T13:19:13.226135825"
     }
 }
\ No newline at end of file
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
index fb8cda2..026a8cd 100644
--- a/tests/PromethION.main.nf.test.snap
+++ b/tests/PromethION.main.nf.test.snap
@@ -2,14 +2,14 @@
     "PromethION data test": {
         "content": [
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-            "multiqc_fastqc.txt:md5,35984961f25a0d4e7352cab4d5650178",
-            "multiqc_general_stats.txt:md5,1465b0b1959e3864b28ecc2340df351b",
-            "multiqc_software_versions.txt:md5,49e3596d49ee49d967d3b6c363b486d5"
+            "multiqc_fastqc.txt:md5,1a4b472e13cadc770832b0e20d1de7b0",
+            "multiqc_general_stats.txt:md5,409cefc7f17f95d176ced6032bf8fb32",
+            "multiqc_software_versions.txt:md5,a3698a2d32e8695c38d50e3d17de5fe3"
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-09-10T08:58:57.180636"
+        "timestamp": "2024-10-28T13:19:57.261730412"
     }
 }
\ No newline at end of file

From 545af046c6660824322f982f4ac322776c25284c Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Mon, 28 Oct 2024 13:38:38 +0000
Subject: [PATCH 57/58] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3aa5bac..b0b12de 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 
 - [#20](https://github.com/nf-core/seqinspector/pull/20) Use tags to generate group reports
 - [#13](https://github.com/nf-core/seqinspector/pull/13) Generate reports per run, per project and per lane.
+- [#49](https://github.com/nf-core/seqinspector/pull/49) Merge with template 3.0.2.
 
 ### `Fixed`
 

From dad5d6d8cf1198273563c7b437b4a37fffed0c66 Mon Sep 17 00:00:00 2001
From: Sarah Griffiths <sarah.griffiths@nanoporetech.com>
Date: Mon, 28 Oct 2024 15:52:49 +0000
Subject: [PATCH 58/58] add seqkit module

---
 assets/multiqc_config.yml |  4 ++--
 docs/output.md            | 13 +++++++++++++
 modules.json              |  5 +++++
 nextflow.config           |  2 +-
 workflows/seqinspector.nf | 10 ++++++++++
 5 files changed, 31 insertions(+), 3 deletions(-)

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index e960d07..ca21520 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/seqinspector/tree/dev" target="_blank">nf-core/seqinspector</a>
+  This report has been generated by the <a href="https://github.com/nf-core/seqinspector/tree/3.0.2" target="_blank">nf-core/seqinspector</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/seqinspector/dev/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/seqinspector/3.0.2/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-seqinspector-methods-description":
     order: -1000
diff --git a/docs/output.md b/docs/output.md
index 15c29ce..6b42a22 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -12,6 +12,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 - [FastQC](#fastqc) - Raw read QC
 - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
+- [SeqkitStats](#seqkitstats) - Per sample TSV file with summary statistics
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
 ### FastQC
@@ -69,6 +70,18 @@ nf-core/seqinspector will generate the following MultiQC reports:
 
 Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see <http://multiqc.info>.
 
+### SeqkitStats
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `seqkit/`
+  - `*.tsv`: Per sample TSV file with summary statistics.
+
+</details>
+
+[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).
+
 ### Pipeline information
 
 <details markdown="1">
diff --git a/modules.json b/modules.json
index 70f3486..da45654 100644
--- a/modules.json
+++ b/modules.json
@@ -14,6 +14,11 @@
                         "branch": "master",
                         "git_sha": "19ca321db5d8bd48923262c2eca6422359633491",
                         "installed_by": ["modules"]
+                    },
+                    "seqkit/stats": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
                     }
                 }
             },
diff --git a/nextflow.config b/nextflow.config
index 70e433a..08f9c6f 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -240,7 +240,7 @@ manifest {
     description     = """Pipeline to QC your sequences"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '1.0dev'
+    version = '3.0.2'
     doi             = ''
 }
 
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 1ba00c6..b0bf95c 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -9,6 +9,8 @@ include { FASTQC                        } from '../modules/nf-core/fastqc/main'
 include { MULTIQC as MULTIQC_GLOBAL     } from '../modules/nf-core/multiqc/main'
 include { MULTIQC as MULTIQC_PER_TAG    } from '../modules/nf-core/multiqc/main'
 
+include { SEQKIT_STATS                  } from '../modules/nf-core/seqkit/stats/main'
+
 include { paramsSummaryMap              } from 'plugin/nf-validation'
 include { paramsSummaryMultiqc          } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 include { softwareVersionsToYAML        } from '../subworkflows/nf-core/utils_nfcore_pipeline'
@@ -138,6 +140,14 @@ workflow SEQINSPECTOR {
         Channel.empty().toList()
     )
 
+    //
+    // MODULE: Run SEQKIT_STATS
+    //
+    SEQKIT_STATS (
+        ch_samplesheet
+    )
+    ch_versions = ch_versions.mix(SEQKIT_STATS.out.versions.first())
+
     emit:
     global_report = MULTIQC_GLOBAL.out.report.toList()      // channel: /path/to/multiqc_report.html
     grouped_reports = MULTIQC_PER_TAG.out.report.toList()   // channel: [ /path/to/multiqc_report.html ]