diff --git a/src/nf_modules/ucsc/main.nf b/src/nf_modules/ucsc/main.nf index 323536a03a03ecdf861a56ea83f3ae6961e08014..28967df579eca6f604506eaba9ebaef9d3b792b5 100644 --- a/src/nf_modules/ucsc/main.nf +++ b/src/nf_modules/ucsc/main.nf @@ -49,9 +49,10 @@ process bigwig_to_wig { script: """ -bigWigToWig ${params.bigwig_to_wig} \ +bigWigToBedGraph ${params.bigwig_to_wig} \ ${bg} \ - ${bg.simpleName}.wig + ${bg.simpleName}.bg +awk '{if(NR>1) {if($1!=lastChrom){printf("variableStep chrom=%s\n",$1);lastChrom=$1;}print $2,$4}}' ${bg.simpleName}.bg > ${bg.simpleName}.wig """ }