diff --git a/src/nf_modules/ucsc/main.nf b/src/nf_modules/ucsc/main.nf index 914697810aa34fe4ebee759ad93a624cf0076cbc..6eeefa835baf2a67726b1718c88d63615be7abc1 100644 --- a/src/nf_modules/ucsc/main.nf +++ b/src/nf_modules/ucsc/main.nf @@ -53,9 +53,7 @@ process wig_to_bedgraph { script: """ -wigToBigWig ${wig} ${wig.simpleName}.bw -bigWigToBedGraph ${wig.simpleName}.bw ${wig.simpleName}.bg -rm ${wig.simpleName}.bw +awk '{print \$1"\\t"\$2-1"\\t"\$2"\\t"\$3}' ${wig} > ${wig.simpleName}.bg """ } @@ -77,12 +75,8 @@ process wig2_to_bedgraph2 { script: """ -wigToBigWig ${wig_a} ${wig_a.simpleName}.bw -bigWigToBedGraph ${wig_a.simpleName}.bw ${wig_a.simpleName}.bg -rm ${wig_a.simpleName}.bw -wigToBigWig ${wig_b} ${wig_b.simpleName}.bw -bigWigToBedGraph ${wig_b.simpleName}.bw ${wig_b.simpleName}.bg -rm ${wig_b.simpleName}.bw +awk '{print \$1"\\t"\$2-1"\\t"\$2"\\t"\$3}' ${wig_a} > ${wig_a.simpleName}.bg +awk '{print \$1"\\t"\$2-1"\\t"\$2"\\t"\$3}' ${wig_b} > ${wig_b.simpleName}.bg """ }