Merge pull request #5 from icgc-argo/payload-gen-update

update payload-gen-variant-calling to 0.2.2.0

Author: junjun-zhang

main.nf

@@ -2,7 +2,7 @@
 nextflow.preview.dsl = 2
 name = 'sanger-wxs-variant-calling'
 short_name = 'sanger-wxs'
-version = '3.1.6-3-1.0'
+version = '3.1.6-3-1.1-dev'
 
 
 /*
@@ -206,7 +206,7 @@ include cavemanVcfFix as cavemanFix from './modules/raw.githubusercontent.com/ic
 include prepSangerSupplement as prepSupp from './modules/raw.githubusercontent.com/icgc-argo/variant-calling-tools/prep-sanger-supplement.0.1.2.0/tools/prep-sanger-supplement/prep-sanger-supplement' params(prepSangerSupplement_params)
 include prepSangerQc as prepQc from './modules/raw.githubusercontent.com/icgc-argo/variant-calling-tools/prep-sanger-qc.0.1.2.0/tools/prep-sanger-qc/prep-sanger-qc' params(prepSangerQc_params)
 include { extractFilesFromTarball as extractVarSnv; extractFilesFromTarball as extractVarIndel; extractFilesFromTarball as extractQC } from './modules/raw.githubusercontent.com/icgc-argo/data-processing-utility-tools/extract-files-from-tarball.0.2.0.0/tools/extract-files-from-tarball/extract-files-from-tarball' params(extractSangerCall_params)
-include { payloadGenVariantCalling as pGenVarSnv; payloadGenVariantCalling as pGenVarIndel; payloadGenVariantCalling as pGenVarSupp; payloadGenVariantCalling as pGenQc } from "./modules/raw.githubusercontent.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling.0.2.0.0/tools/payload-gen-variant-calling/payload-gen-variant-calling" params(payloadGenVariantCall_params)
+include { payloadGenVariantCalling as pGenVarSnv; payloadGenVariantCalling as pGenVarIndel; payloadGenVariantCalling as pGenVarSupp; payloadGenVariantCalling as pGenQc } from "./modules/raw.githubusercontent.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling.0.2.2.0/tools/payload-gen-variant-calling/payload-gen-variant-calling" params(payloadGenVariantCall_params)
 include { songScoreUpload as upSnv; songScoreUpload as upIndel; songScoreUpload as upQc; songScoreUpload as upSupp} from './song-score-utils/song-score-upload' params(upload_params)
 include cleanupWorkdir as cleanup from './modules/raw.githubusercontent.com/icgc-argo/nextflow-data-processing-utility-tools/1.1.5/process/cleanup-workdir'
 

…t-calling/payload-gen-variant-calling.nf …t-calling/payload-gen-variant-calling.nfmodules/raw.githubusercontent.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling.0.2.0.0/tools/payload-gen-variant-calling/payload-gen-variant-calling.nf renamed to modules/raw.githubusercontent.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling.0.2.2.0/tools/payload-gen-variant-calling/payload-gen-variant-calling.nf modules/raw.githubusercontent.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling.0.2.0.0/tools/payload-gen-variant-calling/payload-gen-variant-calling.nf renamed to modules/raw.githubusercontent.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling.0.2.2.0/tools/payload-gen-variant-calling/payload-gen-variant-calling.nf

@@ -22,7 +22,7 @@
  */
 
 nextflow.preview.dsl = 2
-version = '0.2.0.0'
+version = '0.2.2.0'
 
 params.normal_analysis = ""
 params.tumour_analysis = ""
@@ -58,6 +58,7 @@ process payloadGenVariantCalling {
          -f ${files_to_upload} \
          -n ${normal_analysis} \
          -r ${workflow.runName} \
+         -j ${workflow.sessionId} \
          -w ${wf_name} \
          -s ${wf_short_name} \
          -v ${wf_version} ${args_tumour_analysis}