diff --git a/src/nf_modules/ucsc/main.nf b/src/nf_modules/ucsc/main.nf index 999f55fb883cf707ddbbec96d472809a2728753e..f193f0477fc6e0b82bcb1a58747d9368fce5bb2f 100644 --- a/src/nf_modules/ucsc/main.nf +++ b/src/nf_modules/ucsc/main.nf @@ -30,57 +30,3 @@ sort -T ./ -k1,1 -k2,2n ${bg} > \ ${bg.simpleName}_norm.bw """ } - -params.bigwig_to_wig = "" -params.bigwig_to_wig_out = "" -process bigwig_to_wig { - container = "${container_url}" - label "big_mem_mono_cpus" - tag "${file_id}" - if (params.bigwig_to_wig_out != "") { - publishDir "results/${params.bigwig_to_wig_out}", mode: 'copy' - } - - input: - tuple val(file_id) path(bw) - - output: - tuple val(file_id), path("*.wig"), emit: wig - - script: -""" -bigWigToWig ${params.bigwig_to_wig} \ - ${bw} \ - ${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 > ${bw.simpleName}.wig -""" -} - -params.bigwig2_to_wig2 = "" -params.bigwig2_to_wig2_out = "" -process bigwig2_to_wig2 { - container = "${container_url}" - label "big_mem_mono_cpus" - tag "${file_id}" - if (params.bigwig_to_wig_out != "") { - publishDir "results/${params.bigwig_to_wig_out}", mode: 'copy' - } - - input: - tuple val(file_id), path(bw_a), path(bw_b) - - output: - tuple val(file_id), path("${bw_a.simpleName}.wig"), path("${bw_b.simpleName}.wig"), emit: wig - - script: -""" -bigWigToWig ${params.bigwig_to_wig} \ - ${bw_a} \ - ${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}.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