diff --git a/src/nf_modules/danpos/main.nf b/src/nf_modules/danpos/main.nf index a17e2ca1a2d430eea97b1dd4867f1b5ae73237d5..174c4cfd975a92fb54b223bc8cc0eaf49cabc7f9 100644 --- a/src/nf_modules/danpos/main.nf +++ b/src/nf_modules/danpos/main.nf @@ -40,7 +40,7 @@ process dpos_bam { output: tuple val(file_id), path("${file_prefix}/${bam_ip.simpleName}*.wig"), emit: wig - tuple val(file_id), path("${file_prefix}/*.positions.bed"), path("${file_prefix}/*.summit.bed"), emit: bed + tuple val(file_id), path("${file_prefix}/*.positions.bed"), emit: bed tuple val(file_id), path("${file_prefix}"), emit: folder script: @@ -69,7 +69,6 @@ danpos.py dpos -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, "+" }' ${file_prefix}/${bam_ip.simpleName}.bgsub.peaks.xls > ${file_prefix}/${bam_ip.simpleName}.bgsub.positions.bed -awk -v FS='\t' -v OFS='\t' 'FNR > 1 { print \$1, \$4-1, \$4, "Interval_"NR-1, \$6, "+" }' ${file_prefix}/${bam_ip.simpleName}.bgsub.peaks.xls > ${file_prefix}/${bam_ip.simpleName}.bgsub.positions.summit.bed """ } @@ -102,7 +101,7 @@ process dpos_wig { output: tuple val(file_id), path("${file_prefix}/${wig_ip.simpleName}*.wig"), emit: wig - tuple val(file_id), path("${file_prefix}/*.positions.bed"), path("${file_prefix}/*.summit.bed"), emit: bed + tuple val(file_id), path("${file_prefix}/*.positions.bed"), emit: bed tuple val(file_id), path("${file_prefix}"), emit: folder script: @@ -131,7 +130,6 @@ danpos.py dpos -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, "+" }' ${file_prefix}/${bam_ip.simpleName}.bgsub.peaks.xls > ${file_prefix}/${bam_ip.simpleName}.bgsub.positions.bed -awk -v FS='\t' -v OFS='\t' 'FNR > 1 { print \$1, \$4-1, \$4, "Interval_"NR-1, \$6, "+" }' ${file_prefix}/${bam_ip.simpleName}.bgsub.peaks.xls > ${file_prefix}/${bam_ip.simpleName}.bgsub.positions.summit.bed """ } @@ -170,7 +168,7 @@ process dpos_wigvswig { output: tuple val(file_id), path("${file_prefix}/${wig_ip_a.simpleName}*.wig"), emit: wig - tuple val(file_id), path("${file_prefix}/*.positions.bed"), path("${file_prefix}/*.summit.bed"), emit: bed + tuple val(file_id), path("${file_prefix}/*.positions.bed"), emit: bed tuple val(file_id_a), path("${file_prefix}"), emit: folder script: @@ -200,7 +198,6 @@ danpos.py dpos -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, "+" }' ${file_prefix}/${bam_ip.simpleName}.bgsub.peaks.xls > ${file_prefix}/${bam_ip.simpleName}.bgsub.positions.bed -awk -v FS='\t' -v OFS='\t' 'FNR > 1 { print \$1, \$4-1, \$4, "Interval_"NR-1, \$6, "+" }' ${file_prefix}/${bam_ip.simpleName}.bgsub.peaks.xls > ${file_prefix}/${bam_ip.simpleName}.bgsub.positions.summit.bed """ }