diff --git a/src/nf_modules/beagle/main.nf b/src/nf_modules/beagle/main.nf new file mode 100644 index 0000000000000000000000000000000000000000..bc0a54b21d941d358d047334c29d67f4b55be16b --- /dev/null +++ b/src/nf_modules/beagle/main.nf @@ -0,0 +1,23 @@ +version = "5.1_24Aug19.3e8--hdfd78af_1" +container_url = "quay.io/biocontainers/beagle::${version}" + +params.phasing = "" +process phasing { + container = "${container_url}" + label "big_mem_multi_cpus" + tag "$file_id" + + input: + tuple val(file_id), path(vcf) + tuple val(ref_id), path(ref_vcf) + + output: + tuple val(file_id), path("*.bam*"), emit: bam + + script: +""" +beagle nthread=${task.cpus} \ + gtgl=${vcf} \ + ref=${ref_vcf} +""" +}