Merge pull request #14 from icgc-argo/sanger-wgs-variant-calling@2.1.0-9.6.0

[release]

Author: lindaxiang

sanger-wgs-variant-calling/main.nf

@@ -2,7 +2,7 @@
 nextflow.preview.dsl=2
 name='sanger-wgs-variant-calling'
 short_name='sanger-wgs'
-version = '2.1.0-9.5.0'
+version = '2.1.0-9.6.0'
 
 /*
 ========================================================================================
@@ -278,7 +278,7 @@ include { cavemanVcfFix as cavemanFix } from './modules/raw.githubusercontent.co
 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.0.1.3.0/tools/prep-sanger-qc/prep-sanger-qc' params(prepSangerQc_params)
 include { extractFilesFromTarball as extractVarSnv; extractFilesFromTarball as extractVarIndel; extractFilesFromTarball as extractVarCnv; extractFilesFromTarball as extractVarSv } 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 pGenVarCnv; payloadGenVariantCalling as pGenVarSv; payloadGenVariantCalling as pGenVarSupp; payloadGenVariantCalling as pGenQc } from "./wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.5.0/main.nf" params(payloadGenVariantCall_params)
+include { payloadGenVariantCalling as pGenVarSnv; payloadGenVariantCalling as pGenVarIndel; payloadGenVariantCalling as pGenVarCnv; payloadGenVariantCalling as pGenVarSv; payloadGenVariantCalling as pGenVarSupp; payloadGenVariantCalling as pGenQc } from "./wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.6.0/main.nf" params(payloadGenVariantCall_params)
 include { SongScoreUpload as upSnv; SongScoreUpload as upIndel; SongScoreUpload as upCnv; SongScoreUpload as upSv; SongScoreUpload as upQc; SongScoreUpload as upSupp} from './wfpr_modules/github.com/icgc-argo/nextflow-data-processing-utility-tools/song-score-upload@2.6.1/main.nf' params(upload_params)
 include { cleanupWorkdir as cleanup } from './wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/cleanup-workdir@1.0.0/main'
 include { getSecondaryFiles } from './wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/helper-functions@1.0.0/main'

sanger-wgs-variant-calling/pkg.json

@@ -1,6 +1,6 @@
 {
     "name": "sanger-wgs-variant-calling",
-    "version": "2.1.0-9.5.0",
+    "version": "2.1.0-9.6.0",
     "description": "ICGC ARGO Sanger WGS Variant Calling Workflow",
     "main": "main.nf",
     "deprecated": false,
@@ -15,7 +15,7 @@
         "url": "https://github.com/icgc-argo/sanger-wgs-variant-calling.git"
     },
     "dependencies": [
-        "github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.5.0",
+        "github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.6.0",
         "github.com/icgc-argo/data-processing-utility-tools/payload-add-uniform-ids@0.1.1",
         "github.com/icgc-argo/data-processing-utility-tools/helper-functions@1.0.0",
         "github.com/icgc-argo/data-processing-utility-tools/cleanup-workdir@1.0.0",

…-gen-variant-calling@0.5.0/.dockerignore …-gen-variant-calling@0.6.0/.dockerignorewfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.5.0/.dockerignore renamed to wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.6.0/.dockerignore wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.5.0/.dockerignore renamed to wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.6.0/.dockerignore

@@ -25,7 +25,7 @@
 /* this block is auto-generated based on info from pkg.json where   */
 /* changes can be made if needed, do NOT modify this block manually */
 nextflow.enable.dsl = 2
-version = '0.5.0'
+version = '0.6.0'
 
 container = [
     'ghcr.io': 'ghcr.io/icgc-argo/data-processing-utility-tools.payload-gen-variant-calling'

…oad-gen-variant-calling@0.5.0/Dockerfile …oad-gen-variant-calling@0.6.0/Dockerfilewfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.5.0/Dockerfile renamed to wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.6.0/Dockerfile wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.5.0/Dockerfile renamed to wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.6.0/Dockerfile

@@ -43,7 +43,7 @@
     'brass-supplement': ['Structural Variation', ['SV Supplement', None], ['BRASS']],
     'timings-supplement': ['Quality Control Metrics', ['Analysis QC', ['Runtime Stats']], None, None],
     'bas_metrics': ['Quality Control Metrics', ['Aligned Reads QC', ['Alignment Metrics']], ['Sanger:bam_stats']],
-    'contamination_metrics': ['Quality Control Metrics', ['Analysis QC', ['Cross Sample Contamination']], ['Sanger:verifyBamHomChk'], ['GATK:CalculateContamination']],
+    'contamination_metrics': ['Quality Control Metrics', ['Sample QC', ['Cross Sample Contamination']], ['Sanger:verifyBamHomChk'], ['GATK:CalculateContamination']],
     'ascat_metrics': ['Quality Control Metrics', ['Analysis QC', ['Ploidy', 'Tumour Purity']], ['ASCAT']],
     'genotyped_gender_metrics': ['Quality Control Metrics', ['Analysis QC', ['Genotyping Stats']], ['Sanger:compareBamGenotypes']],
     'mutect_filtering_metrics': ['Quality Control Metrics', ['Analysis QC', ['Variant Filtering Stats']], [], ['GATK:FilterMutectCalls']],

…ayload-gen-variant-calling@0.5.0/main.nf …ayload-gen-variant-calling@0.6.0/main.nfwfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.5.0/main.nf renamed to wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.6.0/main.nf wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.5.0/main.nf renamed to wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.6.0/main.nf

@@ -1,6 +1,6 @@
 {
     "name": "payload-gen-variant-calling",
-    "version": "0.5.0",
+    "version": "0.6.0",
     "description": "A tool to generate SONG payloads for variant calling workflows",
     "main": "main.nf",
     "deprecated": false,