danpos: rm position.summit not present for dpos

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
 """
 }