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Fix run merging for unmerged PE data

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This commit is contained in:
James Fellows Yates 2022-04-12 09:25:27 +02:00
parent afb66e445f
commit a5f4fc42d5
2 changed files with 6 additions and 3 deletions
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2
conf/modules.config
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@ -162,7 +162,7 @@ process {
} }
withName: CAT_FASTQ { withName: CAT_FASTQ {
ext.prefix = { "${meta.id}-${meta.run_accession}" } ext.prefix = { "${meta.id}" }
publishDir = [ publishDir = [
path: { "${params.outdir}/run_merging/" }, path: { "${params.outdir}/run_merging/" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,

7
workflows/taxprofiler.nf
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@ -139,7 +139,11 @@ workflow TAXPROFILER {
meta_new.remove('run_accession') meta_new.remove('run_accession')
[ meta_new, reads ] [ meta_new, reads ]
} }
.groupTuple() .groupTuple(by: 0)
.map {
meta, reads ->
[ meta, reads.flatten() ]
}
.branch { .branch {
// we can't concate files if there is not a second run, we branch // we can't concate files if there is not a second run, we branch
// here to separate them out, and mix after // here to separate them out, and mix after
@ -151,7 +155,6 @@ workflow TAXPROFILER {
.mix( ch_reads_for_cat_branch.skip ) .mix( ch_reads_for_cat_branch.skip )
.map { .map {
meta, reads -> meta, reads ->
[ meta, [ reads ].flatten() ] [ meta, [ reads ].flatten() ]
} }