Output channel modification star (#3350)

* feat add channel to emit splice juntions and reads per gene * feat add SJ and ReadsPerGene to stubs out
nf-core · Apr 28, 2023 · 140d5a0 · 140d5a0
1 parent c356ef8
commit 140d5a0
Showing 1 changed file with 4 additions and 0 deletions.
diff --git a/modules/nf-core/star/align/main.nf b/modules/nf-core/star/align/main.nf
@@ -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
@@ -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