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Output channel modification star #3350

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merged 2 commits into from
Apr 28, 2023
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Merged

Output channel modification star #3350

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150b913
feat add channel to emit splice juntions and reads per gene
Lucpen Apr 28, 2023
489eca1
feat add SJ and ReadsPerGene to stubs out
Lucpen Apr 28, 2023
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4 changes: 4 additions & 0 deletions modules/nf-core/star/align/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,8 @@ process STAR_ALIGN {
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('*.tab') , optional:true, emit: tab
tuple val(meta), path('*.SJ.out.tab') , optional:true, emit: spl_junc_tab
tuple val(meta), path('*.ReadsPerGene.out.tab') , optional:true, emit: read_per_gene_tab
tuple val(meta), path('*.out.junction') , optional:true, emit: junction
tuple val(meta), path('*.out.sam') , optional:true, emit: sam
tuple val(meta), path('*.wig') , optional:true, emit: wig
Expand Down Expand Up @@ -87,6 +89,8 @@ process STAR_ALIGN {
touch ${prefix}.unmapped_1.fastq.gz
touch ${prefix}.unmapped_2.fastq.gz
touch ${prefix}.tab
touch ${prefix}.SJ.out.tab
touch ${prefix}.ReadsPerGene.out.tab
touch ${prefix}.Chimeric.out.junction
touch ${prefix}.out.sam
touch ${prefix}.Signal.UniqueMultiple.str1.out.wig
Expand Down