diff --git a/src/nf_modules/danpos/main.nf b/src/nf_modules/danpos/main.nf index 720988de0e9d9f8830c0e7b70ffed4ed79e21dee..7814ec8021ade2ba1bf660948f3b2f54dc5c0a07 100644 --- a/src/nf_modules/danpos/main.nf +++ b/src/nf_modules/danpos/main.nf @@ -181,7 +181,8 @@ process dpeak_bam { tuple val(file_id), path(bam_ip), path(bam_wce) output: - tuple val(file_id), path("${file_prefix}/*.wig"), emit: wig + tuple val(file_id), path("${file_prefix}/${bam_ip.simpleName}.bgsub.wig"), path("${file_prefix}/${bam_wce.simpleName}.wig"), emit: wig + tuple val(file_id), path("${file_prefix}/*.position.bed"), path("${file_prefix}/*.summit.bed"), emit: bed tuple val(file_id), path("${file_prefix}/*.bed"), emit: bed tuple val(file_id), path("${file_prefix}"), emit: folder @@ -241,8 +242,8 @@ process dpeak_wig { tuple val(file_id), path(wig_ip), path(wig_wce) output: - tuple val(file_id), path("${file_prefix}/*.wig"), emit: wig - tuple val(file_id), path("${file_prefix}/*.bed"), emit: bed + tuple val(file_id), path("${file_prefix}/${wig_ip.simpleName}.bgsub.wig"), path("${file_prefix}/${wig_wce.simpleName}.wig"), emit: wig + tuple val(file_id), path("${file_prefix}/*.position.bed"), path("${file_prefix}/*.summit.bed"), emit: bed tuple val(file_id), path("${file_prefix}"), emit: folder script: @@ -272,7 +273,7 @@ danpos.py dpeak -m ${m} \ mv ${file_prefix}/pooled/* ${file_prefix}/ rm -R ${file_prefix}/pooled awk -v FS='\t' -v OFS='\t' 'FNR > 1 { print \$1, \$2-1, \$3, "Interval_"NR-1, \$6, "+" }' ${file_prefix}/${wig_ip.simpleName}.bgsub.peaks.xls > ${file_prefix}/${wig_ip.simpleName}.bgsub.positions.bed -awk -v FS='\t' -v OFS='\t' 'FNR > 1 { print \$1, \$4-1, \$4, "Interval_"NR-1, \$6, "+" }' ${file_prefix}/${wig_ip.simpleName}.bgsub.peaks.xls > ${file_prefix}/${wig_ip.simpleName}.bgsub.positions.summit.bed +awk -v FS='\t' -v OFS='\t' 'FNR > 1 { print \$1, \$4-1, \$4, "Interval_"NR-1, \$6, "+" }' ${file_prefix}/${wig_wce.simpleName}.bgsub.peaks.xls > ${file_prefix}/${wig_ip.simpleName}.bgsub.positions.summit.bed """ }