diff --git a/src/nf_modules/g2gtools/main.nf b/src/nf_modules/g2gtools/main.nf new file mode 100644 index 0000000000000000000000000000000000000000..128e51234632376fbea75e95fe483e2823da1895 --- /dev/null +++ b/src/nf_modules/g2gtools/main.nf @@ -0,0 +1,23 @@ +version = "0.2.8" +container_url = "lbmc/g2gtools:${version}" + +process vci_build { + container = "${container_url}" + label "big_mem_multi_cpus" + tag "$file_id" + + input: + tuple val(file_id), path(vcf) + tuple val(ref_id), path(fasta), path(fai), path(dict) + output: + tuple val(file_id), path("*.chain"), emit: vci + script: +""" +g2gtools vcf2vci \ + -p ${task.cpus} \ + -f ${fasta} \ + -i ${vcf} \ + -s ${file_id} \ + -o ${file_id}.vci +""" +} \ No newline at end of file