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Update main.nf

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Harshil Patel 2020-09-18 10:39:41 +01:00 committed by GitHub
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software/hisat2/align/main.nf
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@ -39,7 +39,7 @@ process HISAT2_ALIGN {
} else if (meta.strandedness == 'reverse') { } else if (meta.strandedness == 'reverse') {
strandedness = meta.single_end ? '--rna-strandness R' : '--rna-strandness RF' strandedness = meta.single_end ? '--rna-strandness R' : '--rna-strandness RF'
} }
def seq_center = params.seq_center ? "--rg-id ${prefix} --rg CN:${params.seq_center.replaceAll('\\s','_')} SM:$prefix" : "--rg-id ${prefix} --rg SM:$prefix" def seq_center = params.seq_center ? "--rg-id ${prefix} --rg SM:$prefix --rg CN:${params.seq_center.replaceAll('\\s','_')}" : "--rg-id ${prefix} --rg SM:$prefix"
if (meta.single_end) { if (meta.single_end) {
def unaligned = params.save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : '' def unaligned = params.save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
""" """