Update for btk plots

.gitattributes

@@ -2,3 +2,5 @@
 *.nf.test linguist-language=nextflow
 modules/nf-core/** linguist-generated
 subworkflows/nf-core/** linguist-generated
+modules/sanger-tol/** linguist-generated
+subworkflows/sanger-tol/** linguist-generated

.nf-core.yml

@@ -24,6 +24,7 @@ lint:
     - .github/workflows/branch.yml
     - .github/CONTRIBUTING.md
     - .github/workflows/linting_comment.yml
+    - .gitattributes
   merge_markers: false
   multiqc_config:
     - report_comment

.pre-commit-config.yaml

@@ -13,15 +13,15 @@ repos:
         exclude: |
           (?x)^(
               .*ro-crate-metadata.json$|
-              modules/nf-core/.*|
-              subworkflows/nf-core/.*|
+              modules/(?!local/).*|
+              subworkflows/(?!local/).*|
               .*\.snap$
           )$
       - id: end-of-file-fixer
         exclude: |
           (?x)^(
               .*ro-crate-metadata.json$|
-              modules/nf-core/.*|
-              subworkflows/nf-core/.*|
+              modules/(?!local/).*|
+              subworkflows/(?!local/).*|
               .*\.snap$
           )$

conf/base.config

@@ -118,6 +118,7 @@ process {
         memory = { 1.GB * Math.pow(4, task.attempt) }
         time   = { 1.h * Math.pow(8, task.attempt) }
     }
+
     withLabel: process_gpu {
         ext.use_gpu = { workflow.profile.contains('gpu') }
         accelerator = { workflow.profile.contains('gpu') ? 1 : null }

conf/modules.config

@@ -17,7 +17,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/repeats/windowmasker" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals("versions.yml") ? null : filename.substring(0, filename.length() - 3) + "obinary" }
+            saveAs: { filename -> filename.substring(0, filename.length() - 3) + "obinary" }
         ]
     }
 
@@ -26,7 +26,6 @@ process {
         publishDir = [
             path: { "${params.outdir}/repeats/windowmasker" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals("versions.yml") ? null : filename }
         ]
     }
 
@@ -54,7 +53,6 @@ process {
         publishDir = [
             path: { "${params.outdir}/read_mapping/${meta.datatype}" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals("versions.yml") ? null : filename }
         ]
     }
 
@@ -78,11 +76,12 @@ process {
         publishDir = [
             path: { "${params.outdir}/read_mapping/${meta.datatype}" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals("versions.yml") ? null : "${meta.id}.coverage.1k.bed.gz" }
+            saveAs: { filename -> "${meta.id}.coverage.1k.bed.gz" }
         ]
     }
 
     withName: "BUSCO_BUSCO" {
+        tag = { "${meta.id}_${lineage}" }
         // Obey "use_work_dir_as_temp", except for large genomes
         scratch = { !params.use_work_dir_as_temp || (meta.genome_size < 2000000000) }
         ext.args = {
@@ -97,10 +96,10 @@ process {
     }
 
     withName: "RESTRUCTUREBUSCODIR" {
+        ext.prefix = { "${meta.id}_${lineage}" }
         publishDir = [
             path: { "${params.outdir}/busco" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals("versions.yml") ? null : filename }
         ]
     }
 
@@ -152,12 +151,14 @@ process {
         ]
     }
 
-    withName: "BLOBTK_IMAGES" {
+    withName: "BLOBTK_PLOT" {
         publishDir = [
             path: { "${params.outdir}/blobtoolkit/plots" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals("versions.yml") ? null : filename }
         ]
+        ext.args    = { "--scale-factor 0.6 ${extra_args.args}" }
+        ext.prefix  = { "${meta.id}_${extra_args.name}" }
     }
 
     withName: "JSONIFY_TAXDUMP" {
@@ -171,9 +172,9 @@ process {
     withName: 'MULTIQC' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [
-            path: { "${params.outdir}/multiqc" },
+            path: { "${params.outdir}" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            saveAs: { filename -> filename.endsWith(".html") ? filename : null }
         ]
     }
 

docs/output.md

@@ -19,7 +19,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 - [Read alignments](#read-alignments) - Aligned reads (optional)
 - [Read coverage](#read-coverage) - Read coverage tracks
 - [Base content](#base-content) - _k_-mer statistics (for k ≤ 4)
-- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
+- [MultiQC report](#multiqc-report) – Aggregate report describing results and QC from the whole pipeline
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
 ### BlobDir
@@ -123,22 +123,15 @@ Those files are the raw data used to build the BlobDir.
 
 </details>
 
-### MultiQC
+### MultiQC report
 
 <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.
+- `multiqc_report.html`: Interactive HTML report summarizing quality metrics from BUSCO.
 
 </details>
 
-[MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarising all samples in your project. Some of the pipeline QC results are visualised in the report and further statistics are available in the report data directory.
-
-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>.
-
 ### Resources / databases
 
 <details markdown="1">

modules.json

@@ -7,47 +7,57 @@
                 "nf-core": {
                     "blast/blastn": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "3a9acfe9865ac6f63bc48667657bfb8293613f56",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/blast/blastn/blast-blastn.diff"
                     },
+                    "blobtk/depth": {
+                        "branch": "master",
+                        "git_sha": "f0ee15907fcece823c1cd5129902405d36108191",
+                        "installed_by": ["modules"]
+                    },
+                    "blobtk/plot": {
+                        "branch": "master",
+                        "git_sha": "02616d1725cc2f97670e25d14d7d1c29d412dffc",
+                        "installed_by": ["modules"]
+                    },
                     "busco/busco": {
                         "branch": "master",
-                        "git_sha": "36c6c8445284e021d95ce30cdf743baef66b21aa",
+                        "git_sha": "25e280b4e6cac8cf6af580e9823264f5bc83cefa",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/busco/busco/busco-busco.diff"
                     },
                     "cat/cat": {
                         "branch": "master",
-                        "git_sha": "69614d4579a6bd9b8a2ecffb35959809d9c36559",
+                        "git_sha": "7ed72ef972290b93d0bdd7c60ff00a693250f77a",
                         "installed_by": ["modules"]
                     },
                     "diamond/blastp": {
                         "branch": "master",
-                        "git_sha": "4012b87ef8f242b7aa1eb17e165aa003b86b49c0",
+                        "git_sha": "422966026b45f2852cbe1a919dadc52082bf62f1",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/diamond/blastp/diamond-blastp.diff"
                     },
                     "diamond/blastx": {
                         "branch": "master",
-                        "git_sha": "4012b87ef8f242b7aa1eb17e165aa003b86b49c0",
+                        "git_sha": "8d52ac1b6f035f46c005a27b3510873c2a67ea41",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/diamond/blastx/diamond-blastx.diff"
                     },
                     "fastawindows": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "a3a12a5bf8fb088f5bc68bbb053811b51762abea",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/fastawindows/fastawindows.diff"
                     },
                     "gunzip": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "96c57dfd98a0641886a67bd449fe33ee2ec0e374",
                         "installed_by": ["modules"]
                     },
                     "minimap2/align": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "5c9f8d5b7671237c906abadc9ff732b301ca15ca",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/minimap2/align/minimap2-align.diff"
                     },
@@ -58,45 +68,45 @@
                     },
                     "pigz/compress": {
                         "branch": "master",
-                        "git_sha": "447f7bc0fa41dfc2400c8cad4c0291880dc060cf",
+                        "git_sha": "c908ccaf0a5c802b6f8e814d8c5cf85da2364222",
                         "installed_by": ["modules"]
                     },
                     "samtools/flagstat": {
                         "branch": "master",
-                        "git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
+                        "git_sha": "156feda0cb6589cd29c04902004fa3b53bc00205",
                         "installed_by": ["modules"]
                     },
                     "samtools/index": {
                         "branch": "master",
-                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
+                        "git_sha": "156feda0cb6589cd29c04902004fa3b53bc00205",
                         "installed_by": ["modules"]
                     },
                     "samtools/view": {
                         "branch": "master",
-                        "git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
+                        "git_sha": "156feda0cb6589cd29c04902004fa3b53bc00205",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/samtools/view/samtools-view.diff"
                     },
                     "seqtk/subseq": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "a46713779030a5f508117080cbf4b693dd4c6e33",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/seqtk/subseq/seqtk-subseq.diff"
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "447f7bc0fa41dfc2400c8cad4c0291880dc060cf",
                         "installed_by": ["modules"]
                     },
                     "windowmasker/mkcounts": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "git_sha": "ed6f7d2e090911f69f0f3af563f5af9ba1fc1fa0",
+                        "installed_by": ["repeat_masking"]
                     },
                     "windowmasker/ustat": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "git_sha": "ed6f7d2e090911f69f0f3af563f5af9ba1fc1fa0",
+                        "installed_by": ["repeat_masking"]
                     }
                 }
             },
@@ -119,6 +129,26 @@
                     }
                 }
             }
+        },
+        "https://github.com/sanger-tol/nf-core-modules.git": {
+            "modules": {
+                "sanger-tol": {
+                    "restructurebuscodir": {
+                        "branch": "main",
+                        "git_sha": "8dac7d789fb5ec033c38e69c2553e71cae0dd4c3",
+                        "installed_by": ["modules"]
+                    }
+                }
+            },
+            "subworkflows": {
+                "sanger-tol": {
+                    "repeat_masking": {
+                        "branch": "main",
+                        "git_sha": "45230473d69437a6048b5436d74ce464a5cc8d27",
+                        "installed_by": ["subworkflows"]
+                    }
+                }
+            }
         }
     }
 }

modules/local/generate_config.nf

@@ -6,12 +6,12 @@ process GENERATE_CONFIG {
     container "docker.io/genomehubs/blobtoolkit:4.4.6"
 
     input:
+    // Some data files are passed as "val" because we need to know the original paths. Staging would prevent that
     tuple val(meta), val(fasta)
     val taxon_query
     val busco_lin
     tuple val(metabn), path(blastn)
     path lineage_tax_ids
-    // The following are passed as "val" because we need to know the original paths. Staging would prevent that
     val reads
     val db_paths