Merge pull request #396 from genomic-medicine-sweden/wgsmetricsupdate

Add constraints to block the pipeline from running CollectWgsMetrics on WES samples
nf-core · Aug 4, 2023 · b1ad334 · b1ad334
2 parents 0839494 + cb2dfaf
commit b1ad334
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -17,6 +17,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Invalid GATK4 container which caused incorrect singularity downloads with nf-core download [nf-core/modules #3668](https://github.com/nf-core/modules/issues/3668)
 - Make the default cram prefix same as markduplicates prefix [#392](https://github.com/nf-core/raredisease/pull/392)
+- Added constraints to block the pipeline from running CollectWgsMetrics on WES samples [#396](https://github.com/nf-core/raredisease/pull/396)
 
 ## v1.1.1 - Abu (Patch) [2023-07-26]
 

diff --git a/conf/modules/qc_bam.config b/conf/modules/qc_bam.config
@@ -52,22 +52,22 @@ process {
     }
 
     withName: '.*QC_BAM:PICARD_COLLECTWGSMETRICS' {
-        ext.when = params.aligner.equals("bwamem2")
+        ext.when = { params.analysis_type.equals("wgs") && params.aligner.equals("bwamem2") }
         ext.prefix = { "${meta.id}_wgsmetrics" }
     }
 
     withName: '.*QC_BAM:PICARD_COLLECTWGSMETRICS_Y' {
-        ext.when = params.aligner.equals("bwamem2")
+        ext.when = { params.analysis_type.equals("wgs") && params.aligner.equals("bwamem2") }
         ext.prefix = { "${meta.id}_wgsmetrics_y" }
     }
 
     withName: '.*QC_BAM:SENTIEON_WGSMETRICS' {
-        ext.when = params.aligner.equals("sentieon")
+        ext.when = { params.analysis_type.equals("wgs") && params.aligner.equals("sentieon") }
         ext.prefix = { "${meta.id}_wgsmetrics" }
     }
 
     withName: '.*QC_BAM:SENTIEON_WGSMETRICS_Y' {
-        ext.when = params.aligner.equals("sentieon")
+        ext.when = { params.analysis_type.equals("wgs") && params.aligner.equals("sentieon") }
         ext.prefix = { "${meta.id}_wgsmetrics_y" }
     }
 }