Germline variant payload

modules/icgc-argo-workflows/payload/germlinevariant/main.nf

@@ -0,0 +1,43 @@
+process PAYLOAD_GERMLINEVARIANT {
+    tag "$meta.id"
+    label 'process_single'
+
+
+    conda "bioconda::multiqc=1.13"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
+        'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"
+
+    input:  // input, make update as needed
+      tuple val(meta), path(files_to_upload), path(metadata_analysis)
+      path pipeline_yml
+      val tarball
+
+
+    output:  // output, make update as needed
+      tuple val(meta), path("*.payload.json"), path("out/*"), emit: payload_files
+      path "versions.yml", emit: versions
+
+    script:
+      // add and initialize variables here as needed
+      def arg_pipeline_yml = pipeline_yml.name != 'NO_FILE' ? "-p $pipeline_yml" : ''
+      """
+      main.py \
+        -f ${files_to_upload} \
+        -a ${metadata_analysis} \
+        -b "${meta.genomeBuild}" \
+        -w "DNA Seq Germline Variant Workflow" \
+        -r ${workflow.runName} \
+        -s "${workflow.sessionId}" \
+        -v "${workflow.manifest.version}" \
+        -t "${meta.tool}" \
+        -l "${tarball}" \
+        -d "${meta.dataType}" \
+        $arg_pipeline_yml
+
+      cat <<-END_VERSIONS > versions.yml
+      "${task.process}":
+          python: \$(python --version | sed 's/Python //g')
+      END_VERSIONS
+      """
+  }

modules/icgc-argo-workflows/payload/germlinevariant/meta.yml

@@ -0,0 +1,60 @@
+name: "payload_germlinevariant"
+## TODO nf-core: Add a description of the module and list keywords
+description: write your description here
+keywords:
+  - sort
+tools:
+  - "payload_germlinevariant":
+      description: "A simple wrapper written in `nextflow` for the payload generation tool to generate ARGO Song payloads containing QC metrics files."
+      licence: ["MIT"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+
+  - files_to_upload:
+      type: file
+      description: QC metrics files
+
+  - metadata_analysis:
+      type: file
+      description: Song metadata in JSON format
+
+  - genome_annotation:
+      type: string
+      description: genome annotation name
+
+  - genome_build:
+      type: string
+      description: genome build name
+
+  - path pipeline_yml:
+      type: file
+      description: yml file collect from CUSTOM_DUMPSOFTWAREVERSIONS
+  - tool:
+      type: string
+      description: name of tool
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+
+  - payload_files:
+      type: file
+      description: Generated payload and QC files with normalized names
+
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+
+
+authors:
+  - "@edsu7"