diff --git a/src/nf_modules/ucsc/main.nf b/src/nf_modules/ucsc/main.nf new file mode 100644 index 0000000000000000000000000000000000000000..c63de6e227707552f5d51c3b0fc4cda34d9b8186 --- /dev/null +++ b/src/nf_modules/ucsc/main.nf @@ -0,0 +1,26 @@ +version = "407" +container_url = "lbmc/ucsc:${version}" + +process bedgraph_to_bigwig { + container = "${container_url}" + label "big_mem_mono_cpus" + tag "${file_id}" + + input: + tuple val(file_id) path(bg) + tuple val(file_id) path(bed) + + output: + tuple val(file_id), path("*.bw"), emit: fasta + + script: +""" +# transform bed file of start-stop chromosome size to stop chromosome size +awk -v OFS="\\t" '{print \$1, \$3}' ${bed} > chromsize.txt + +bedGraphToBigWig ${bg} \ + chromsize.txt \ + ${bg.simpleName}_norm.bw +""" +} +