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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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Kevin Menden 2021-01-26 12:46:30 +01:00 committed by GitHub
parent 5be1598b29
commit 8e2749beb7
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1 changed files with 3 additions and 3 deletions
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software/star/align/main.nf
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@ -33,7 +33,7 @@ process STAR_ALIGN {
tuple val(meta), path('*sortedByCoord.out.bam') , optional:true, emit: bam_sorted tuple val(meta), path('*sortedByCoord.out.bam') , optional:true, emit: bam_sorted
tuple val(meta), path('*toTranscriptome.out.bam'), optional:true, emit: bam_transcript tuple val(meta), path('*toTranscriptome.out.bam'), optional:true, emit: bam_transcript
tuple val(meta), path('*Aligned.unsort.out.bam'), optional:true, emit: bam_unsorted tuple val(meta), path('*Aligned.unsort.out.bam') , optional:true, emit: bam_unsorted
tuple val(meta), path('*fastq.gz') , optional:true, emit: fastq tuple val(meta), path('*fastq.gz') , optional:true, emit: fastq
tuple val(meta), path('*.tab') , optional:true, emit: tab tuple val(meta), path('*.tab') , optional:true, emit: tab
@ -55,7 +55,7 @@ process STAR_ALIGN {
$seq_center \\ $seq_center \\
$options.args $options.args
${mv_unsorted_bam} $mv_unsorted_bam
if [ -f ${prefix}.Unmapped.out.mate1 ]; then if [ -f ${prefix}.Unmapped.out.mate1 ]; then
mv ${prefix}.Unmapped.out.mate1 ${prefix}.unmapped_1.fastq mv ${prefix}.Unmapped.out.mate1 ${prefix}.unmapped_1.fastq