diff --git a/sanger-wxs-variant-calling/main.nf b/sanger-wxs-variant-calling/main.nf index 39888e0..51ff64b 100755 --- a/sanger-wxs-variant-calling/main.nf +++ b/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' diff --git a/sanger-wxs-variant-calling/pkg.json b/sanger-wxs-variant-calling/pkg.json index 16df042..dff3eb9 100644 --- a/sanger-wxs-variant-calling/pkg.json +++ b/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", diff --git a/sanger-wxs-variant-calling/tests/local-test.local-2.nf.json b/sanger-wxs-variant-calling/tests/local-test.local-2.nf.json new file mode 100644 index 0000000..b4f6760 --- /dev/null +++ b/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" + } +} diff --git a/wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.4.0/.dockerignore b/wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.5.0/.dockerignore similarity index 100% rename from wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.4.0/.dockerignore rename to wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.5.0/.dockerignore diff --git a/wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.4.0/Dockerfile b/wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.5.0/Dockerfile similarity index 100% rename from wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.4.0/Dockerfile rename to wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.5.0/Dockerfile diff --git a/wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.4.0/main.nf b/wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.5.0/main.nf similarity index 98% rename from wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.4.0/main.nf rename to wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.5.0/main.nf index 9c2f2a0..fe43912 100755 --- a/wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.4.0/main.nf +++ b/wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.5.0/main.nf @@ -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' diff --git a/wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.4.0/main.py b/wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.5.0/main.py similarity index 94% rename from wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.4.0/main.py rename to wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.5.0/main.py index 8c93d95..fbcb325 100755 --- a/wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.4.0/main.py +++ b/wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.5.0/main.py @@ -33,7 +33,7 @@ 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']], @@ -41,13 +41,13 @@ '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) diff --git a/wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.4.0/nextflow.config b/wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.5.0/nextflow.config similarity index 100% rename from wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.4.0/nextflow.config rename to wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.5.0/nextflow.config diff --git a/wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.4.0/pkg.json b/wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.5.0/pkg.json similarity index 97% rename from wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.4.0/pkg.json rename to wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.5.0/pkg.json index 560dcd4..1fa4ea7 100644 --- a/wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.4.0/pkg.json +++ b/wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.5.0/pkg.json @@ -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" -} +} \ No newline at end of file diff --git a/wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.4.0/wfpr_modules b/wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.5.0/wfpr_modules similarity index 100% rename from wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.4.0/wfpr_modules rename to wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/payload-gen-variant-calling@0.5.0/wfpr_modules