Merge pull request #979 from mskcc/bugfix/workflow_logic_issues

Bugfix/workflow logic issues
mskcc · Mar 16, 2023 · 1d215b4 · 1d215b4
2 parents 2a50a7c + 0c9c547
commit 1d215b4
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Showing 2 changed files with 10 additions and 10 deletions.
diff --git a/dsl2.nf b/dsl2.nf
@@ -57,7 +57,7 @@ WFs = params.workflows instanceof Boolean ? '' : params.workflows
 
 WFs = WFs.split(',').collect{it.trim().toLowerCase()}.unique()
 
-WFs = (!params.mapping && !params.bamMapping && aggregateParamIsFile) ? ['snv','sv','mutsig','germSNV','germSV','lohhla','facets','qc','msisensor'] : WFs
+WFs = (!params.mapping && !params.bamMapping && aggregateParamIsFile) ? ['snv','sv','mutsig','germsnv','germsv','lohhla','facets','qc','msisensor'] : WFs
 
 workflow {
   //Set flags for when each pipeline is required to run.

diff --git a/modules/subworkflow/sampleQC_wf.nf b/modules/subworkflow/sampleQC_wf.nf
@@ -14,15 +14,15 @@ workflow sampleQC_wf
     referenceMap = params.referenceMap
     targetsMap   = params.targetsMap
 
-    inputChannel.map{ idSample, target, bam, bai ->
-        [idSample, target, bam, bai, targetsMap."$target".targetsInterval,  targetsMap."$target".baitsInterval]
-    }.set{ bamsBQSR4HsMetrics }
-
-    QcCollectHsMetrics(bamsBQSR4HsMetrics,
-                       Channel.value([referenceMap.genomeFile, referenceMap.genomeIndex, referenceMap.genomeDict]))
-
-    if (params.assayType == "exome"){
-	collectHsMetricsOutput = QcCollectHsMetrics.out.collectHsMetricsOutput
+    if (params.assayType != "genome"){
+        inputChannel.map{ idSample, target, bam, bai ->
+            [idSample, target, bam, bai, targetsMap."$target".targetsInterval,  targetsMap."$target".baitsInterval]
+        }.set{ bamsBQSR4HsMetrics }
+
+        QcCollectHsMetrics(bamsBQSR4HsMetrics,
+                           Channel.value([referenceMap.genomeFile, referenceMap.genomeIndex, referenceMap.genomeDict])
+                          )
+        collectHsMetricsOutput = QcCollectHsMetrics.out.collectHsMetricsOutput
     } else {
     	inputChannel
         	.map{ idSample, target, bam, bai -> [idSample, ""]}