Merge pull request #16 from icgc-argo/sanger-wxs-variant-calling@3.1.6-3.5.0

[release]

Author: junjun-zhang

sanger-wxs-variant-calling/main.nf

@@ -2,7 +2,7 @@
 nextflow.enable.dsl = 2
 name = 'sanger-wxs-variant-calling'
 short_name = 'sanger-wxs'
-version = '3.1.6-3.4.0'
+version = '3.1.6-3.5.0'
 
 
 /*
@@ -226,7 +226,7 @@ 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 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 "./wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.4.0/main" params(payloadGenVariantCall_params)
+include { payloadGenVariantCalling as pGenVarSnv; payloadGenVariantCalling as pGenVarIndel; 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" params(payloadGenVariantCall_params)
 include { SongScoreUpload as upSnv; SongScoreUpload as upIndel; 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-wxs-variant-calling/pkg.json

@@ -1,6 +1,6 @@
 {
     "name": "sanger-wxs-variant-calling",
-    "version": "3.1.6-3.4.0",
+    "version": "3.1.6-3.5.0",
     "description": "ICGC ARGO Sanger WXS Variant Calling Workflow",
     "main": "main.nf",
     "deprecated": false,
@@ -14,7 +14,7 @@
         "url": "https://github.com/icgc-argo/sanger-wxs-variant-calling.git"
     },
     "dependencies": [
-        "github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.4.0",
+        "github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.5.0",
         "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",

sanger-wxs-variant-calling/tests/local-test.local-2.nf.json

@@ -0,0 +1,21 @@
+{
+  "study_id": "TEST-PR",
+  "tumour_aln_metadata": "data/03905962-f1e1-41e8-9059-62f1e1c1e8fc.analysis.json",
+  "tumour_aln_cram": "data/SA610229.103.20200320.wxs.grch38.cram",
+  "tumour_extra_info": "data/T.SA610229.tsv",
+  "normal_aln_metadata": "data/9940db0f-c100-496a-80db-0fc100d96ac1.analysis.json",
+  "normal_aln_cram": "data/SA610228.67.20200319.wxs.grch38.cram",
+  "normal_extra_info": "data/N.SA610228.tsv",
+  "publish_dir": "outdir",
+  "sangerWxsVariantCaller": {
+    "cpus": 10,
+    "mem": 50,
+    "exclude": "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr22,chrX,chrY,chrUn%,HLA%,%_alt,%_random,chrM,chrEBV",
+    "vagrent_annot": "/home/ubuntu/references/sanger/VAGrENT_ref_GRCh38_hla_decoy_ebv_ensembl_91.tar.gz",
+    "ref_genome_tar": "/home/ubuntu/references/sanger/core_ref_GRCh38_hla_decoy_ebv.tar.gz",
+    "ref_snv_indel_tar": "/home/ubuntu/references/sanger/SNV_INDEL_ref_GRCh38_hla_decoy_ebv-fragment.tar.gz"  
+  },
+  "generateBas": {
+    "ref_genome_fa": "/home/ubuntu/references/grch38/GRCh38_hla_decoy_ebv.fa"
+  }
+}

…-gen-variant-calling@0.4.0/.dockerignore …-gen-variant-calling@0.5.0/.dockerignorewfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.4.0/.dockerignore renamed to wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.5.0/.dockerignore wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.4.0/.dockerignore renamed to wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.5.0/.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 = '0.4.0'  // package version
+version = '0.5.0'
 
 container = [
     'ghcr.io': 'ghcr.io/icgc-argo/data-processing-utility-tools.payload-gen-variant-calling'

…oad-gen-variant-calling@0.4.0/Dockerfile …oad-gen-variant-calling@0.5.0/Dockerfilewfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.4.0/Dockerfile renamed to wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.5.0/Dockerfile wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.4.0/Dockerfile renamed to wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.5.0/Dockerfile

@@ -33,21 +33,21 @@
 
 
 variant_type_to_data_type_etc = {
-    'snv': ['Simple Nucleotide Variation', ['Raw SNV Calls', None], ['CaVEMan'], ['GATK:Mutect2']],   # dataCategory, [dataType, data_subtype], analysis_tools
+    'snv': ['Simple Nucleotide Variation', ['Raw SNV Calls', None], ['CaVEMan'], ['GATK:Mutect2']],   # dataCategory, [dataType, data_subtypes], analysis_tools
     'indel': ['Simple Nucleotide Variation', ['Raw InDel Calls', None], ['Pindel'], ['GATK:Mutect2']],
     'cnv': ['Copy Number Variation', ['Raw CNV Calls', None], ['ASCAT']],
     'sv': ['Structural Variation', ['Raw SV Calls', None], ['BRASS']],
     'caveman-supplement': ['Simple Nucleotide Variation', ['SNV Supplement', None], ['CaVEMan']],
     'pindel-supplement': ['Simple Nucleotide Variation', ['InDel Supplement', None], ['Pindel']],
     'ascat-supplement': ['Copy Number Variation', ['CNV Supplement', None], ['ASCAT']],
     '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']],
-    'ascat_metrics': ['Quality Control Metrics', ['Analysis QC', 'Ploidy and Purity Estimation'], ['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']],
-    'mutect_callable_metrics': ['Quality Control Metrics', ['Analysis QC', 'Variant Callable Stats'], [], ['GATK:Mutect2']],
+    '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']],
+    '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']],
+    'mutect_callable_metrics': ['Quality Control Metrics', ['Analysis QC', ['Variant Callable Stats']], [], ['GATK:Mutect2']],
 }
 
 workflow_full_name = {
@@ -151,22 +151,22 @@ def get_files_info(file_to_upload, wf_short_name,  wf_version, somatic_or_germli
 
     file_info['info'] = {
         'data_category': variant_type_to_data_type_etc[variant_type][0],
-        'data_subtype': None
+        'data_subtypes': None
     }
 
     extra_info = {}
     if new_fname.endswith('.vcf.gz'):
         file_info['dataType'] = variant_type_to_data_type_etc[variant_type][1][0]
-        file_info['info']['data_subtype'] = variant_type_to_data_type_etc[variant_type][1][1]
+        file_info['info']['data_subtypes'] = variant_type_to_data_type_etc[variant_type][1][1]
     elif new_fname.endswith('.vcf.gz.tbi'):
         file_info['dataType'] = 'VCF Index'
     elif new_fname.endswith('.tgz'):
         if new_fname.endswith('-supplement.tgz'):
             file_info['dataType'] = variant_type_to_data_type_etc[variant_type][1][0]
-            file_info['info']['data_subtype'] = variant_type_to_data_type_etc[variant_type][1][1]
+            file_info['info']['data_subtypes'] = variant_type_to_data_type_etc[variant_type][1][1]
         elif new_fname.endswith('_metrics.tgz'):
             file_info['dataType'] = variant_type_to_data_type_etc[variant_type][1][0]
-            file_info['info']['data_subtype'] = variant_type_to_data_type_etc[variant_type][1][1]
+            file_info['info']['data_subtypes'] = variant_type_to_data_type_etc[variant_type][1][1]
         else:
             sys.exit('Error: unknown file type "%s"' % file_to_upload)
 

…ayload-gen-variant-calling@0.4.0/main.nf …ayload-gen-variant-calling@0.5.0/main.nfwfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.4.0/main.nf renamed to wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.5.0/main.nf wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.4.0/main.nf renamed to wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.5.0/main.nf

@@ -1,6 +1,6 @@
 {
     "name": "payload-gen-variant-calling",
-    "version": "0.4.0",
+    "version": "0.5.0",
     "description": "A tool to generate SONG payloads for variant calling workflows",
     "main": "main.nf",
     "deprecated": false,
@@ -33,4 +33,4 @@
     "license": "GNU Affero General Public License v3",
     "bugReport": "https://github.com/icgc-argo/data-processing-utility-tools/issues",
     "homepage": "https://github.com/icgc-argo/data-processing-utility-tools#readme"
-}
+}