diff --git a/src/nf_modules/ucsc/main.nf b/src/nf_modules/ucsc/main.nf index 6ce54f0d7684d830f1276a4d998611f40cb09e76..06ac54f0bab935af92b6a4079dd693bfa6108f5b 100644 --- a/src/nf_modules/ucsc/main.nf +++ b/src/nf_modules/ucsc/main.nf @@ -35,6 +35,28 @@ sort -T ./ -k1,1 -k2,2n ${bg} > \ """ } +params.wig2bedgraph = "" +params.wig2bedgraph_out = "" +process wig2bedgraph { + container = "${container_url}" + label "big_mem_mono_cpus" + tag "${file_id}" + if (params.wig2bedgraph_out != "") { + publishDir "results/${params.wig2bedgraph_out}", mode: 'copy' + } + + input: + tuple val(file_id) path(wig) + + output: + tuple val(file_id), path("*.bg"), emit: bedgraph + + script: +""" +wigToBedGraph ${wig} ${wig.simpleName}.bg +""" +} + params.wig_to_bedgraph = "" params.wig_to_bedgraph_out = "" process wig_to_bedgraph {