Fix more config selectors

pinin4fjords · pinin4fjords · commit 1bc1b73bdf7e · 2024-12-12T10:53:15.000Z
diff --git a/workflows/rnaseq/nextflow.config b/workflows/rnaseq/nextflow.config
@@ -140,7 +140,7 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
                 ]
             }
 
-            withName: 'NFCORE_RNASEQ:RNASEQ:BAM_DEDUP_UMI_(STAR|HISAT2):BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX' {
+            withName: 'NFCORE_RNASEQ:RNASEQ:BAM_DEDUP_UMI_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX' {
                 publishDir = [
                     path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
                     mode: params.publish_dir_mode,
@@ -149,7 +149,7 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
                 ]
             }
 
-            withName: 'NFCORE_RNASEQ:RNASEQ:BAM_DEDUP_UMI_(STAR|HISAT2):BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:.*' {
+            withName: 'NFCORE_RNASEQ:RNASEQ:BAM_DEDUP_UMI_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:.*' {
                 ext.prefix = { "${meta.id}.transcriptome.sorted.bam" }
                 publishDir = [
                     path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}/samtools_stats" : params.outdir },

Original file line number	Diff line number	Diff line change
`@@ -140,7 +140,7 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {`
`140`	`140`	`]`
`141`	`141`	`}`
`142`	`142`
`143`		`- withName: 'NFCORE_RNASEQ:RNASEQ:BAM_DEDUP_UMI_(STAR\|HISAT2):BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX' {`
	`143`	`+ withName: 'NFCORE_RNASEQ:RNASEQ:BAM_DEDUP_UMI_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX' {`
`144`	`144`	`publishDir = [`
`145`	`145`	`path: { params.save_align_intermeds \|\| params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },`
`146`	`146`	`mode: params.publish_dir_mode,`
`@@ -149,7 +149,7 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {`
`149`	`149`	`]`
`150`	`150`	`}`
`151`	`151`
`152`		`- withName: 'NFCORE_RNASEQ:RNASEQ:BAM_DEDUP_UMI_(STAR\|HISAT2):BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:.*' {`
	`152`	`+ withName: 'NFCORE_RNASEQ:RNASEQ:BAM_DEDUP_UMI_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:.*' {`
`153`	`153`	`ext.prefix = { "${meta.id}.transcriptome.sorted.bam" }`
`154`	`154`	`publishDir = [`
`155`	`155`	`path: { params.save_align_intermeds \|\| params.save_umi_intermeds ? "${params.outdir}/${params.aligner}/samtools_stats" : params.outdir },`