diff --git a/src/nf_modules/agat/main.nf b/src/nf_modules/agat/main.nf new file mode 100644 index 0000000000000000000000000000000000000000..03b1a3f58d7b1f7d10d63feb2ef571d84ee9842a --- /dev/null +++ b/src/nf_modules/agat/main.nf @@ -0,0 +1,23 @@ +version = "0.8.0" +container_url = "lbmc/agat:${version}" + +params.gff_to_bed = "" +params.gff_to_bed_out = "" +process gff_to_bed { + container = "${container_url}" + label "big_mem_mono_cpus" + tag "$file_id" + if (params.gff_to_bed_out != "") { + publishDir "results/${params.gff_to_bed_out}", mode: 'copy' + } + + input: + tuple val(file_id), path(gff) + output: + tuple val(file_id), path("*.bed"), emit: bed + + script: +""" +agat_convert_sp_gff2bed.pl --gff ${gff} -o ${gff.simpleName}.bed +""" +} \ No newline at end of file