several improvements

nf-core · Oct 29, 2024 · 7e41b19 · 7e41b19
1 parent d8c31ec
commit 7e41b19
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Showing 6 changed files with 56 additions and 23 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -22,6 +22,15 @@ process {
         ext.args = '--quiet'
     }
 
+    withName: UNTAR {
+        publishDir = [
+            path: { "${params.outdir}/kraken2_db" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            enabled: params.save_uncompressed_k2db
+        ]
+    }
+
     withName: 'MULTIQC_GLOBAL' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [

diff --git a/modules.json b/modules.json
@@ -8,32 +8,44 @@
                     "fastqc": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "kraken2/kraken2": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "krona/ktimporttaxonomy": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "krona/ktupdatetaxonomy": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "untar": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     }
                 }
             },
@@ -42,20 +54,26 @@
                     "utils_nextflow_pipeline": {
                         "branch": "master",
                         "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082",
-                        "installed_by": ["subworkflows"]
+                        "installed_by": [
+                            "subworkflows"
+                        ]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
                         "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba",
-                        "installed_by": ["subworkflows"]
+                        "installed_by": [
+                            "subworkflows"
+                        ]
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
                         "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e",
-                        "installed_by": ["subworkflows"]
+                        "installed_by": [
+                            "subworkflows"
+                        ]
                     }
                 }
             }
         }
     }
-}
+}
diff --git a/nextflow.config b/nextflow.config
@@ -23,6 +23,7 @@ params {
     kraken2_db                 = 'https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/kraken2/testdb-kraken2.tar.gz'
     kraken2_save_reads         = false
     kraken2_save_readclassifications = false
+    save_uncompressed_k2db     = false
 
     // MultiQC options
     multiqc_config             = null

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -255,5 +255,10 @@
         {
             "$ref": "#/$defs/generic_options"
         }
-    ]
+    ],
+    "properties": {
+        "save_uncompressed_k2db": {
+            "type": "boolean"
+        }
+    }
 }
diff --git a/subworkflows/local/phylogenetic_qc.nf b/subworkflows/local/phylogenetic_qc.nf
@@ -12,18 +12,18 @@ workflow PHYLOGENETIC_QC{
     reads
 
     main:
-    ch_reads = reads
-    ch_multiqc_files = Channel.empty()
-    ch_versions             = Channel.empty()
+    ch_reads    = reads
+    ch_versions = Channel.empty()
     //
     // MODULE: Untar kraken2_db or read it as it is if not compressed
     //
     if (params.kraken2_db.endsWith('.gz')) {
         UNTAR_KRAKEN2_DB ( [ [:], params.kraken2_db ])
         ch_kraken2_db = UNTAR_KRAKEN2_DB.out.untar.map { it[1] }
-        ch_versions      = ch_versions.mix(UNTAR_KRAKEN2_DB.out.versions)
+        ch_versions      = ch_versions.mix(UNTAR_KRAKEN2_DB.out.versions.first())
     } else {
-        ch_kraken2_db = Channel.value([[:], file(params.kraken2_db, checkIfExists: true)])
+        ch_kraken2_db = Channel.fromPath(params.kraken2_db, checkIfExists: true)
+        ch_kraken2_db = ch_kraken2_db.collect()
     }
 
     //
@@ -35,9 +35,7 @@ workflow PHYLOGENETIC_QC{
         params.kraken2_save_reads,
         params.kraken2_save_readclassifications
     )
-    ch_multiqc_files       = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.report )
-    ch_versions            = ch_versions.mix( KRAKEN2_KRAKEN2.out.versions.first() )
-    //KRAKEN2_KRAKEN2.out.report.map { meta, report -> [ report ] }.collect()
+    ch_versions            = ch_versions.mix( KRAKEN2_KRAKEN2.out.versions.first())
 
     //
     // MODULE: krona plot the kraken2 reports
@@ -50,6 +48,6 @@ workflow PHYLOGENETIC_QC{
 
     emit:
     versions        = ch_versions
-    mqc             = ch_multiqc_files
+    mqc             = KRAKEN2_KRAKEN2.out.report
     krona_plots     = KRONA_KTIMPORTTAXONOMY.out.html.collect()
 }
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
@@ -46,15 +46,16 @@ workflow SEQINSPECTOR {
     PHYLOGENETIC_QC (
         ch_samplesheet
     )
-    //ch_multiqc_files = ch_multiqc_files.mix(PHYLOGENETIC_QC.out.mqc.collect{it[1]}.ifEmpty([]))
-    ch_versions = ch_versions.mix(PHYLOGENETIC_QC.out.versions)
+    // TODO: Uncomment this line for add the kraken2 report to the MultiQC (channel creation might need some further tweaking)
+    //ch_multiqc_files = ch_multiqc_files.mix(PHYLOGENETIC_QC.out)
+    ch_versions = ch_versions.mix(PHYLOGENETIC_QC.out.versions.flatten())
 
 
     //
     // Collate and save software versions
     //
     softwareVersionsToYAML(ch_versions)
-        .collectFile(
+            .collectFile(
             storeDir: "${params.outdir}/pipeline_info",
             name: 'nf_core_'  + 'pipeline_software_' +  'mqc_'  + 'versions.yml',
             sort: true,
@@ -92,6 +93,7 @@ workflow SEQINSPECTOR {
         )
     )
 
+    //            .map { meta, file -> file }
     MULTIQC_GLOBAL (
         ch_multiqc_files
             .map { meta, file -> file }