add example of variant calling with gatk4

src/example_variant_calling.nf

+nextflow.enable.dsl=2
+
+/*
+Testing pipeline for marseq scRNASeq analysis
+*/
+
+include {
+  mapping;
+} from "./nf_modules/bwa/main.nf"
+
+include {
+  mapping;
+} from "./nf_modules/gatk4/main.nf" addParams(
+  variant_calling_out: "vcf/",
+)
+
+channel
+  .fromFilePairs( params.fastq, size: -1)
+  .set { fastq_files }
+channel
+  .fromPath( params.fasta )
+  .ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" }
+  .map { it -> [it.simpleName, it]}
+  .set { fasta_files }
+
+workflow {
+  mapping(fasta, fastq_files)
+  germline_cohort_data_variant_calling(mapping.out.bam, fasta)
+}

src/nf_modules/gatk4/main.nf

@@ -10,6 +10,7 @@ include {
   mark_duplicate;
 } from './nf_modules/picard/main.nf'
 
+params.variant_calling_out = ""
 workflow germline_cohort_data_variant_calling {
   take:
     bam
@@ -234,6 +235,9 @@ process genomic_db_call {
   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(db)
     tuple val(ref_id), path(fasta), path(fai), path(dict)