src/pipelines/nf_modules/peak_calling.nf: changes in bedtools_slop and bedtools_merge

src/pipelines/nf_modules/peak_calling.nf

@@ -86,7 +86,7 @@ process bedtools_slop {
     ${new_id}.enlarged.tmp.bed
     sort -k 1,1 -k2,2n ${new_id}.enlarged.tmp.bed > ${new_id}.enlarged.sort.bed
     bedtools merge -i ${new_id}.enlarged.sort.bed \
-    -d 6 -c 5,6 -o mean,distinct | awk '{print \$1"\\t"\$2"\\t"\$3"\\tpeak_"NR"\\t"\$4"\\t"\$5}' > ${new_id}.merged.bed
+    -c 5,6 -o mean,distinct | awk '{print \$1"\\t"\$2"\\t"\$3"\\tpeak_"NR"\\t"\$4"\\t"\$5}' > ${new_id}.merged.bed
     """
 }
 
@@ -135,7 +135,7 @@ process bedtools_merge {
     """
     cat *.bed | sort -k1,1 -k2,2n > tmp.bed
     bedtools merge -i tmp.bed \
-    -d 6 -c 1,5,6 -o count,mean,distinct | awk '{if(\$4 >= 2){print \$1"\\t"\$2"\\t"\$3"\\tpeak_"NR"\\t"\$5"\\t"\$6}}' > ${sp}.rep_merged.bed
+    -c 1,5,6 -o count,mean,distinct | awk '{if(\$4 >= 2){print \$1"\\t"\$2"\\t"\$3"\\tpeak_"NR"\\t"\$5"\\t"\$6}}' > ${sp}.rep_merged.bed
     """
 }