gatk4: add gvcf to variant_calling_out

src/nf_modules/gatk4/main.nf

@@ -159,6 +159,10 @@ process call_variants_per_sample {
   container = "${container_url}"
   label "big_mem_mono_cpus"
   tag "$file_id"
+  if (params.variant_calling_out != "") {
+    publishDir "results/${params.variant_calling_out}", mode: 'copy'
+  }
+
   input:
     tuple val(file_id), path(bam), path(bam_idx)
     tuple val(ref_id), path(fasta), path(fai), path(dict)