enable qc when starting from VC

CHANGELOG.md

@@ -15,6 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Changed
 
 - [#1339](https://github.com/nf-core/sarek/pull/1339) - Update sentieon-modules
+- [#1344](https://github.com/nf-core/sarek/pull/1344) - Enable CRAM QC, when starting from variantcalling
 
 ### Fixed
 

conf/modules/modules.config

@@ -78,12 +78,12 @@ process {
         ]
     }
 
-    if ((params.step == 'mapping' || params.step == 'markduplicates'|| params.step == 'prepare_recalibration'|| params.step == 'recalibrate') && (!(params.skip_tools && params.skip_tools.split(',').contains('baserecalibrator')))) {
-        withName: 'NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH' {
+    if (!(params.skip_tools && params.skip_tools.split(',').contains('baserecalibrator'))) {
+        withName: 'NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH' {
             ext.prefix = { "${meta.id}.recal" }
         }
 
-        withName: 'NFCORE_SAREK:SAREK:CRAM_QC_RECAL:SAMTOOLS_STATS' {
+        withName: 'NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS' {
             ext.prefix = { "${meta.id}.recal.cram" }
             ext.when   = { !(params.skip_tools && params.skip_tools.split(',').contains('samtools')) }
             publishDir = [

subworkflows/local/cram_sampleqc/main.nf

@@ -1,15 +1,32 @@
-include { BAM_NGSCHECKMATE } from '../../../subworkflows/nf-core/bam_ngscheckmate/main'
-
+include { BAM_NGSCHECKMATE                           } from '../../../subworkflows/nf-core/bam_ngscheckmate/main'
+include { CRAM_QC_MOSDEPTH_SAMTOOLS as CRAM_QC_RECAL } from '../../../subworkflows/local/cram_qc_mosdepth_samtools/main'
 workflow CRAM_SAMPLEQC {
 
     take:
-    ch_cram             // channel: [ val(meta), cram, crai ]
-    ngscheckmate_bed    // channel: [ ngscheckmate_bed ]
-    fasta               // channel: [ fasta ]
+    ch_cram                     // channel: [ val(meta), cram, crai ]
+    ngscheckmate_bed            // channel: [ ngscheckmate_bed ]
+    fasta                       // channel: [ fasta ]
+    skip_baserecalibration      // boolean:
+    intervals_for_preprocessing // channel:
 
     main:
 
     ch_versions = Channel.empty()
+    reports     = Channel.empty()
+
+    if(!skip_baserecalibration){
+
+        CRAM_QC_RECAL(
+            ch_cram,
+            fasta,
+            intervals_for_preprocessing)
+
+        // Gather QC reports
+        reports = CRAM_QC_RECAL.out.reports.collect{ meta, report -> report }
+
+        // Gather used softwares versions
+        ch_versions = ch_versions.mix(CRAM_QC_RECAL.out.versions)
+    }
 
     ch_ngscheckmate_bed = ngscheckmate_bed.map{bed -> [[id: "ngscheckmate"], bed]}
 
@@ -24,6 +41,7 @@ workflow CRAM_SAMPLEQC {
     all          = BAM_NGSCHECKMATE.out.all          // channel: [ meta, all ]
     vcf          = BAM_NGSCHECKMATE.out.vcf          // channel: [ meta, vcf ]
     pdf          = BAM_NGSCHECKMATE.out.pdf          // channel: [ meta, pdf ]
+    reports
 
     versions = ch_versions                     // channel: [ versions.yml ]
 }

tests/test_cnvkit.yml

@@ -57,6 +57,30 @@
       md5sum: b4a49faf170e436ec32dcc21ccc3ce8f
     - path: results/cnvkit
       should_exist: false
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt
+      md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt
+      md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt
+      md5sum: 103098d0bf76ed82d2b87d5f242b099a
+    - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz
+      md5sum: b5888cf7395c57d39879a5faa6159eb3
+    - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi
+      md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
+    - path: results/reports/samtools/sample3/sample3.recal.cram.stats
+    # conda changes md5sums for test
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt
+      md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt
+      md5sum: 39005ffaac22871ffaaf19656fe69c5b
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt
+      md5sum: 68d4b98f17361fddf73052ead34fa370
+    - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz
+      md5sum: 2819e995eafded35f53328c4ec19ba58
+    - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi
+      md5sum: 393c2749068304d8545b501b9d4658e4
+    - path: results/reports/samtools/sample4/sample4.recal.cram.stats
+    # conda changes md5sums for test
 - name: Run variant calling on tumor_only sample with cnvkit
   command: nextflow run main.nf -profile test_cache,tools_tumoronly --tools cnvkit --outdir results
   tags:
@@ -88,6 +112,17 @@
       md5sum: e6d0190c1c37ce6e41f76ca5b24ccca3
     - path: results/cnvkit
       should_exist: false
+    - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt
+      md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
+    - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.region.dist.txt
+      md5sum: 39005ffaac22871ffaaf19656fe69c5b
+    - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt
+      md5sum: 68d4b98f17361fddf73052ead34fa370
+    - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz
+      md5sum: 2819e995eafded35f53328c4ec19ba58
+    - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi
+      md5sum: 393c2749068304d8545b501b9d4658e4
+    - path: results/reports/samtools/sample2/sample2.recal.cram.stats
 - name: Run variant calling on germline sample with cnvkit
   command: nextflow run main.nf -profile test_cache,tools_germline --tools cnvkit --outdir results
   tags:
@@ -121,6 +156,17 @@
       md5sum: 79aae7e9c135fb8c65f8fbda12610faf
     - path: results/cnvkit
       should_exist: false
+    - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt
+      md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
+    - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.region.dist.txt
+      md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
+    - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt
+      md5sum: 103098d0bf76ed82d2b87d5f242b099a
+    - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz
+      md5sum: b5888cf7395c57d39879a5faa6159eb3
+    - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz.csi
+      md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
+    - path: results/reports/samtools/sample1/sample1.recal.cram.stats
 - name: Run variant calling on somatic samples with cnvkit and skip variant calling on matched normal
   command: nextflow run main.nf -profile test_cache,tools_somatic --tools cnvkit --only_paired_variant_calling --outdir results
   tags:
@@ -156,3 +202,27 @@
       md5sum: d15bf5061d90c8edbcba04d2bd2a270c
     - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
       md5sum: b4a49faf170e436ec32dcc21ccc3ce8f
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt
+      md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt
+      md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt
+      md5sum: 103098d0bf76ed82d2b87d5f242b099a
+    - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz
+      md5sum: b5888cf7395c57d39879a5faa6159eb3
+    - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi
+      md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
+    - path: results/reports/samtools/sample3/sample3.recal.cram.stats
+    # conda changes md5sums for test
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt
+      md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt
+      md5sum: 39005ffaac22871ffaaf19656fe69c5b
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt
+      md5sum: 68d4b98f17361fddf73052ead34fa370
+    - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz
+      md5sum: 2819e995eafded35f53328c4ec19ba58
+    - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi
+      md5sum: 393c2749068304d8545b501b9d4658e4
+    - path: results/reports/samtools/sample4/sample4.recal.cram.stats
+    # conda changes md5sums for test

tests/test_controlfreec.yml

@@ -52,6 +52,30 @@
       should_exist: false
     - path: results/cnvkit
       should_exist: false
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt
+      md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt
+      md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt
+      md5sum: 103098d0bf76ed82d2b87d5f242b099a
+    - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz
+      md5sum: b5888cf7395c57d39879a5faa6159eb3
+    - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi
+      md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
+    - path: results/reports/samtools/sample3/sample3.recal.cram.stats
+    # conda changes md5sums for test
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt
+      md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt
+      md5sum: 39005ffaac22871ffaaf19656fe69c5b
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt
+      md5sum: 68d4b98f17361fddf73052ead34fa370
+    - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz
+      md5sum: 2819e995eafded35f53328c4ec19ba58
+    - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi
+      md5sum: 393c2749068304d8545b501b9d4658e4
+    - path: results/reports/samtools/sample4/sample4.recal.cram.stats
+    # conda changes md5sums for test
 - name: Run variant calling on somatic samples with controlfreec without intervals
   command: nextflow run main.nf -profile test_cache,tools_somatic --tools controlfreec --no_intervals -stub-run --outdir results
   tags:
@@ -105,6 +129,26 @@
       should_exist: false
     - path: results/mpileup
       should_exist: false
+    - path: results/reports/mosdepth/sample3/sample3.recal.global.dist.txt
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/mosdepth/sample3/sample3.recal.summary.txt
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz.csi
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/samtools/sample3/sample3.recal.cram.stats
+    # conda changes md5sums for test
+    - path: results/reports/mosdepth/sample4/sample4.recal.global.dist.txt
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/mosdepth/sample4/sample4.recal.summary.txt
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz.csi
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/samtools/sample4/sample4.recal.cram.stats
+    # conda changes md5sums for test
 - name: Run variant calling on tumor_only sample with controlfreec
   command: nextflow run main.nf -profile test_cache,tools_tumoronly --tools controlfreec -stub-run --outdir results
   tags:
@@ -148,3 +192,14 @@
       should_exist: false
     - path: results/mpileup
       should_exist: false
+    - path: results/reports/mosdepth/sample2/sample2.recal.global.dist.txt
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/mosdepth/sample2/sample2.recal.region.dist.txt
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/mosdepth/sample2/sample2.recal.summary.txt
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/samtools/sample2/sample2.recal.cram.stats