diff --git a/src/nf_modules/ucsc/main.nf b/src/nf_modules/ucsc/main.nf index 6e0c016d568c8004bca29a792b26d900b22bda38..e3076ebd60c27bbb24907a65868ffaeadc7b9271 100644 --- a/src/nf_modules/ucsc/main.nf +++ b/src/nf_modules/ucsc/main.nf @@ -78,4 +78,49 @@ bedgraph_to_wig.pl --bedgraph ${bw_a.simpleName}.bg --wig ${bw_a.simpleName}.wig bigWigToBedGraph ${bw_b} ${bw_b.simpleName}.bg bedgraph_to_wig.pl --bedgraph ${bw_b.simpleName}.bg --wig ${bw_b.simpleName}.wig --step 10 """ +} + +params.wig_to_bigwig = "" +params.wig_to_bigwig_out = "" +process wig_to_bigwig { + container = "${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(w) + + output: + tuple val(file_id), path("${bw.simpleName}.bw"), emit: bw + + script: +""" +wigToBigWig ${w} ${w.simpleName}.bw +""" +} + +params.wig2_to_bigwig2 = "" +params.wig2_to_bigwig2_out = "" +process wig2_to_bigwig2 { + container = "${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(w_a), path(w_b) + + output: + tuple val(file_id), path("${bw_a.simpleName}.bw"), path("${bw_b.simpleName}.bw"), emit: bw + + script: +""" +wigToBigWig ${w_a} ${w_a.simpleName}.bw +wigToBigWig ${w_b} ${w_b.simpleName}.bw +""" } \ No newline at end of file