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updating meta.sex type check #559

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merged 2 commits into from
May 28, 2024
Merged

updating meta.sex type check #559

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6974324
updating meta.sex type check
jemten May 27, 2024
6ec160f
switching equals to matches
jemten May 27, 2024
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2 changes: 1 addition & 1 deletion conf/modules/generate_cytosure_files.config
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Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,7 @@ process {

withName: '.*GENERATE_CYTOSURE_FILES:VCF2CYTOSURE' {
ext.args = { [
meta.sex.equals(1) ? '--sex male' : '--sex female',
meta.sex.equals('1') ? '--sex male' : '--sex female',
'--size 5000',
'--maxbnd 5000'
].join(' ') }
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4 changes: 2 additions & 2 deletions subworkflows/local/gens.nf
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Expand Up @@ -36,8 +36,8 @@ workflow GENS {

COLLECTREADCOUNTS.out.hdf5
.branch { meta, counts ->
female: meta.sex.equals(2) || meta.sex.equals(0)
male: meta.sex.equals(1)
female: meta.sex.matches('2|other')
male: meta.sex.equals('1')
}
.set { ch_denoisereadcounts_in }

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