Merge pull request #395 from genomic-medicine-sweden/update-config

Make target bed file optional for WGS mode
nf-core · Aug 4, 2023 · ccd6a79 · ccd6a79
2 parents b1ad334 + aea0b73
commit ccd6a79
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Showing 3 changed files with 7 additions and 6 deletions.
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)
+- Make target bed file optional for WGS mode (Issue [#375](https://github.com/nf-core/raredisease/issues/375)) [#395](https://github.com/nf-core/raredisease/pull/395)
 - 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/prepare_references.config b/conf/modules/prepare_references.config
@@ -86,28 +86,28 @@ process {
     }
 
     withName: '.*PREPARE_REFERENCES:TABIX_PT' {
-        ext.when = { params.target_bed && params.target_bed.endsWith(".gz") }
+        ext.when = { !params.target_bed.equals(null) && params.target_bed.endsWith(".gz") }
     }
 
     withName: '.*PREPARE_REFERENCES:TABIX_PBT' {
-        ext.when = { params.target_bed && !params.target_bed.endsWith(".gz") }
+        ext.when = { !params.target_bed.equals(null) && !params.target_bed.endsWith(".gz") }
     }
 
     withName: '.*PREPARE_REFERENCES:GATK_BILT' {
-        ext.when = { params.target_bed }
+        ext.when = { !params.target_bed.equals(null) }
         ext.prefix = { "${meta.id}_target" }
     }
 
     withName: '.*PREPARE_REFERENCES:GATK_ILT' {
-        ext.when = { params.target_bed }
+        ext.when = { !params.target_bed.equals(null) }
         ext.args = { "--PADDING ${params.bait_padding} -SUBDIVISION_MODE INTERVAL_SUBDIVISION --SCATTER_COUNT 2" }
         publishDir = [
             enabled: false
         ]
     }
 
     withName: '.*PREPARE_REFERENCES:CAT_CAT_BAIT' {
-        ext.when = { params.target_bed }
+        ext.when = { !params.target_bed.equals(null) }
         ext.prefix = { "${meta.id}" }
     }
 

diff --git a/conf/modules/qc_bam.config b/conf/modules/qc_bam.config
@@ -29,7 +29,7 @@ process {
     }
 
     withName: '.*QC_BAM:PICARD_COLLECTHSMETRICS' {
-        ext.when = { params.target_bed }
+        ext.when = { !params.target_bed.equals(null) }
         ext.prefix = { "${meta.id}_hsmetrics" }
     }