diff --git a/subworkflows/local/dedup_umis.nf b/subworkflows/local/dedup_umis.nf index ebc9e726..6ff16757 100644 --- a/subworkflows/local/dedup_umis.nf +++ b/subworkflows/local/dedup_umis.nf @@ -48,19 +48,17 @@ workflow DEDUP_UMIS { BAMTOOLS_SPLIT ( in_bam ) ch_versions = ch_versions.mix(BAMTOOLS_SPLIT.out.versions.first()) ch_split_bam = BAMTOOLS_SPLIT.out.bam - .map{ - meta, bam -> - [bam] + .map { meta, bam -> + [bam] } .flatten() - .map{ - bam -> - def bam_basename = bam.toString().split('/')[-1] - def split_bam_basename = bam_basename.split(/\./) - def new_meta = [ - 'id': split_bam_basename.take(split_bam_basename.size()-1).join("."), - ] - [ new_meta, bam ] + .map { bam -> + def bam_basename = bam.toString().split('/')[-1] + def split_bam_basename = bam_basename.split(/\./) + def new_meta = [ + 'id': split_bam_basename.take(split_bam_basename.size()-1).join("."), + ] + [ new_meta, bam ] } } else { @@ -81,11 +79,10 @@ workflow DEDUP_UMIS { in_bam .join(in_bai) .combine(GROUP_TRANSCRIPTS.out.grouped_transcripts.flatten()) - .map{ - meta, bam, bai, region -> - def region_basename = region.toString().split('/')[-1] - def split_region_basename = region_basename.split(/\./) - [['id': meta.id + "." + split_region_basename[0]], bam, bai, region] + .map { meta, bam, bai, region -> + def region_basename = region.toString().split('/')[-1] + def split_region_basename = region_basename.split(/\./) + [['id': meta.id + "." + split_region_basename[0]], bam, bai, region] } ) ch_split_bam = SPLIT_BAM.out.split_bam @@ -147,11 +144,10 @@ workflow DEDUP_UMIS { // SAMTOOLS_MERGE ( ch_dedup_bam - .map{ - meta, bam -> - def bam_basename = bam.toString().split('/')[-1] - def split_bam_basename = bam_basename.split(/\./) - def new_meta = [ 'id': split_bam_basename[0] ] + .map { meta, bam -> + def bam_basename = bam.toString().split('/')[-1] + def split_bam_basename = bam_basename.split(/\./) + def new_meta = [ 'id': split_bam_basename[0] ] [ new_meta, bam ] } .groupTuple(),