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Bugfix/workflow logic issues #979

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merged 4 commits into from
Mar 16, 2023
Merged

Bugfix/workflow logic issues #979

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967f643
set workflow list to all lowercase when --workflows is empty
anoronh4 Dec 19, 2022
a659dcc
removed 'mutsig' label from list of inputs that can turn on the loh w…
anoronh4 Dec 19, 2022
cf107d7
moved QcCollectHsMetrics invocation to a conditional closure so that …
anoronh4 Dec 22, 2022
0c9c547
Revert "removed 'mutsig' label from list of inputs that can turn on t…
anoronh4 Dec 22, 2022
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2 changes: 1 addition & 1 deletion dsl2.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -54,7 +54,7 @@ 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.
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18 changes: 9 additions & 9 deletions modules/subworkflow/sampleQC_wf.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -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, ""]}
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