diff --git a/src/nf_modules/ucsc/main.nf b/src/nf_modules/ucsc/main.nf index e88f35a2419d5f7271605adcbe43c454e2952758..999f55fb883cf707ddbbec96d472809a2728753e 100644 --- a/src/nf_modules/ucsc/main.nf +++ b/src/nf_modules/ucsc/main.nf @@ -49,10 +49,10 @@ process bigwig_to_wig { script: """ -bigWigToBedGraph ${params.bigwig_to_wig} \ +bigWigToWig ${params.bigwig_to_wig} \ ${bw} \ - ${bg.simpleName}.bg -awk '{if(NR>1) {if(\$1!=lastChrom){printf("variableStep chrom=%s span=1\\n",\$1);lastChrom=\$1;}print \$2,\$4}}' ${bw.simpleName}.bg > ${bw.simpleName}.wig + ${bg.simpleName}.raw +awk '{if(NR>1) {if(\$1!=lastChrom){printf("variableStep chrom=%s span=1\\n",\$1);lastChrom=\$1;}print \$2,\$4}}' ${bw.simpleName}.raw > ${bw.simpleName}.wig """ } @@ -74,13 +74,13 @@ process bigwig2_to_wig2 { script: """ -bigWigToBedGraph ${params.bigwig_to_wig} \ +bigWigToWig ${params.bigwig_to_wig} \ ${bw_a} \ - ${bw_a.simpleName}.bg -awk '{if(NR>1) {if(\$1!=lastChrom){printf("variableStep chrom=%s span=1\\n",\$1);lastChrom=\$1;}print \$2,\$4}}' ${bw_a.simpleName}.bg > ${bw_a.simpleName}.wig + ${bw_a.simpleName}.raw +awk '{if(NR>1) {if(\$1!=lastChrom){printf("variableStep chrom=%s span=1\\n",\$1);lastChrom=\$1;}print \$2,\$4}}' ${bw_a.simpleName}.raw > ${bw_a.simpleName}.wig bigWigToBedGraph ${params.bigwig_to_wig} \ ${bw_b} \ - ${bw_b.simpleName}.bg -awk '{if(NR>1) {if(\$1!=lastChrom){printf("variableStep chrom=%s span=1\\n",\$1);lastChrom=\$1;}print \$2,\$4}}' ${bw_b.simpleName}.bg > ${bw_b.simpleName}.wig + ${bw_b.simpleName}.raw +awk '{if(NR>1) {if(\$1!=lastChrom){printf("variableStep chrom=%s span=1\\n",\$1);lastChrom=\$1;}print \$2,\$4}}' ${bw_b.simpleName}.raw > ${bw_b.simpleName}.wig """ } \ No newline at end of file