danpos: add xls > bed convertion

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("${file_prefix}/pooled/*.wig"), emit: wig
+    tuple val(file_id), path("${file_prefix}/*.wig"), emit: wig
+    tuple val(file_id), path("${file_prefix}/*.bed"), emit: bed
     tuple val(file_id), path("${file_prefix}"), emit: folder
 
   script:
@@ -208,6 +209,10 @@ danpos.py dpeak -m ${m} \
   -b ${bam_wce} \
   -o ${file_prefix} \
   ${bam_ip}
+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
 """
 }
 
@@ -236,7 +241,8 @@ process dpeak_wig {
     tuple val(file_id), path(wig_ip), path(wig_wce)
 
   output:
-  tuple val(file_id), path("${file_prefix}/pooled/*.wig"), emit: wig
+  tuple val(file_id), path("${file_prefix}/*.wig"), emit: wig
+  tuple val(file_id), path("${file_prefix}/*.bed"), emit: bed
   tuple val(file_id), path("${file_prefix}"), emit: folder
 
   script:
@@ -263,6 +269,10 @@ danpos.py dpeak -m ${m} \
   -b ${wig_wce} \
   -o ${file_prefix} \
   ${wig_ip}
+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
 """
 }