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allow storeDir for RunBQSR #1001

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allow storeDir for RunBQSR #1001

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6f78a3a
remove non-path and non-context variables from output channels
anoronh4 Dec 27, 2023
264ced1
fix bug
anoronh4 Dec 27, 2023
cfe13d7
fix overlapping file issue in AlignReads for outputs that share the s…
anoronh4 Dec 31, 2023
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13 changes: 7 additions & 6 deletions pipeline.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -581,8 +581,7 @@ if (params.mapping) {
referenceMap.knownIndelsIndex
])
output:
set idSample, target, file("${idSample}.bam"), file("${idSample}.bam.bai") into bamsBQSR4Alfred, bamsBQSR4CollectHsMetrics, bamsBQSR4Tumor, bamsBQSR4Normal, bamsBQSR4QcPileup, bamsBQSR4Qualimap
set idSample, target, val("${file(outDir).toString()}/bams/${idSample}/${idSample}.bam"), val("${file(outDir).toString()}/bams/${idSample}/${idSample}.bam.bai") into bamResults
set idSample, target, file("${idSample}.bam"), file("${idSample}.bam.bai") into bamsBQSR4Alfred, bamsBQSR4CollectHsMetrics, bamsBQSR4Tumor, bamsBQSR4Normal, bamsBQSR4QcPileup, bamsBQSR4Qualimap, bamResults
file("file-size.txt") into bamSize
script:
if (workflow.profile == "juno") {
Expand Down Expand Up @@ -661,13 +660,15 @@ if (params.mapping) {
"""
}

File file = new File(outname)
file.newWriter().withWriter { w ->
File file_bammapping = new File(outname)
file_bammapping.newWriter().withWriter { w ->
w << "SAMPLE\tTARGET\tBAM\tBAI\n"
}

bamResults.subscribe { Object obj ->
file.withWriterAppend { out ->
bamResults.map{ idSample, target, bam, bai ->
[ idSample, target, "${file(outDir).toString()}/bams/${idSample}/${idSample}.bam", "${file(outDir).toString()}/bams/${idSample}/${idSample}.bam.bai" ]
}.subscribe { Object obj ->
file_bammapping.withWriterAppend { out ->
out.println "${obj[0]}\t${obj[1]}\t${obj[2]}\t${obj[3]}"
}
}
Expand Down