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lindaxianglindaxiang
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change dataType and add genome annotation version into payload
1 parent eb7aa84 commit 34e2b12

11 files changed

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‎payload-gen-variant-processing/Dockerfile‎

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FROM python:3.7.5-slim-buster
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LABEL org.opencontainers.image.source https://github.com/icgc-argo/data-processing-utility-tools
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LABEL org.opencontainers.image.source https://github.com/icgc-argo-workflows/data-processing-utility-tools
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RUN apt-get update && apt-get install -y procps jq
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‎payload-gen-variant-processing/main.nf‎

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version = '0.3.0'
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container = [
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'ghcr.io': 'ghcr.io/icgc-argo/data-processing-utility-tools.payload-gen-variant-processing'
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'ghcr.io': 'ghcr.io/icgc-argo-workflows/data-processing-utility-tools.payload-gen-variant-processing'
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]
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default_container_registry = 'ghcr.io'
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/********************************************************************/

‎payload-gen-variant-processing/main.py‎

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import copy
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variant_type_to_data_type_etc = {
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'snv': ['Simple Nucleotide Variation', 'Raw SNV Calls', ['CaVEMan', 'Bcftools:view'], ['GATK:Mutect2', 'Bcftools:view']], # dataCategory, dataType, analysis_tools
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'indel': ['Simple Nucleotide Variation', 'Raw InDel Calls', ['Pindel', 'Bcftools:view'], ['GATK:Mutect2', 'Bcftools:view']]
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'snv': ['Simple Nucleotide Variation', 'Filtered SNV Calls', ['CaVEMan', 'Bcftools:view'], ['GATK:Mutect2', 'Bcftools:view']], # dataCategory, dataType, analysis_tools
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'indel': ['Simple Nucleotide Variation', 'Filtered InDel Calls', ['Pindel', 'Bcftools:view'], ['GATK:Mutect2', 'Bcftools:view']]
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}
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workflow_full_name = {
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'analysis_type': input_analysis_type
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}
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],
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'genome_build': 'GRCh38_hla_decoy_ebv'
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'genome_build': 'GRCh38_hla_decoy_ebv',
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'genome_annotation': 'GENCODE v38'
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},
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'variant_class': analysis.get('variant_class')
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}

‎payload-gen-variant-processing/pkg.json‎

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],
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"repository": {
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"type": "git",
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"url": "https://github.com/icgc-argo/data-processing-utility-tools.git"
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"url": "https://github.com/icgc-argo-workflows/data-processing-utility-tools.git"
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},
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"container": {
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"registries": [
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{
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"registry": "ghcr.io",
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"type": "docker",
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"org": "icgc-argo",
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"org": "icgc-argo-workflows",
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"default": true
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}
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]
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}
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],
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"license": "GNU Affero General Public License v3",
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"bugReport": "https://github.com/icgc-argo/data-processing-utility-tools/issues",
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"homepage": "https://github.com/icgc-argo/data-processing-utility-tools#readme"
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"bugReport": "https://github.com/icgc-argo-workflows/data-processing-utility-tools/issues",
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"homepage": "https://github.com/icgc-argo-workflows/data-processing-utility-tools#readme"
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}

‎payload-gen-variant-processing/tests/checker.nf‎

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version = '0.3.0'
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container = [
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'ghcr.io': 'ghcr.io/icgc-argo/data-processing-utility-tools.payload-gen-variant-processing'
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'ghcr.io': 'ghcr.io/icgc-argo-workflows/data-processing-utility-tools.payload-gen-variant-processing'
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]
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default_container_registry = 'ghcr.io'
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/********************************************************************/

‎payload-gen-variant-processing/tests/expected/expected.gatk-mutect2.filtered.snv.payload.json‎

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"Bcftools:view"
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]
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},
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"dataType": "Raw SNV Calls"
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"dataType": "Filtered SNV Calls"
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},
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{
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"fileName": "TEST-PR.DO250183.SA610229.wgs.20200922.gatk-mutect2.somatic.snv.open-filter.vcf.gz.tbi",
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"workflow": {
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"workflow_name": "Open Access Variant Filtering",
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"workflow_short_name": "open-filter",
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"workflow_version": "0.1.0",
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"run_id": "maniac_saha",
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"session_id": "cb4d9dc6-d0b2-4998-bfae-80976e1ded55",
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"workflow_version": "0.3.0",
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"run_id": "focused_goodall",
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"session_id": "2fce03b6-006a-4fe5-9578-b0ecc139b40c",
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"inputs": [
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{
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"input_analysis_id": "ca105e4d-d16b-461c-905e-4dd16b861cc8",
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"analysis_type": "variant_calling"
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}
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],
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"genome_build": "GRCh38_hla_decoy_ebv"
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"genome_build": "GRCh38_hla_decoy_ebv",
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"genome_annotation": "GENCODE v38"
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},
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"variant_class": "Somatic"
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}

‎payload-gen-variant-processing/tests/expected/expected.sanger-wgs.filtered.snv.payload.json‎

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"Bcftools:view"
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]
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},
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"dataType": "Raw SNV Calls"
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"dataType": "Filtered SNV Calls"
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},
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{
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"fileName": "TEST-PR.DO250183.SA610229.wgs.20200513.sanger-wgs.somatic.snv.open-filter.vcf.gz.tbi",
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"workflow": {
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"workflow_name": "Open Access Variant Filtering",
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"workflow_short_name": "open-filter",
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"workflow_version": "0.1.0",
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"run_id": "insane_rubens",
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"session_id": "b5dbc2b3-f915-4f56-acbb-97d31df6c1f0",
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"workflow_version": "0.3.0",
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"run_id": "zen_rubens",
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"session_id": "12b3e3ed-ce27-40f5-a5d3-8b41315b262e",
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"inputs": [
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{
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"input_analysis_id": "3414534a-47a4-492d-9453-4a47a4192d6d",
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"analysis_type": "variant_calling"
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}
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],
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"genome_build": "GRCh38_hla_decoy_ebv"
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"genome_build": "GRCh38_hla_decoy_ebv",
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"genome_annotation": "GENCODE v38"
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},
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"variant_class": "Somatic",
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"info": {
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"origin": "ICGC-25K"
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},
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"variant_class": "Somatic"
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}
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}

‎payload-gen-variant-processing/tests/expected/expected.sanger-wxs.filtered.indel.payload.json‎

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"Bcftools:view"
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]
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},
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"dataType": "Raw InDel Calls"
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"dataType": "Filtered InDel Calls"
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},
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{
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"fileName": "TEST-PR.DO250183.SA610229.wxs.20200911.sanger-wxs.somatic.indel.open-filter.vcf.gz.tbi",
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"workflow": {
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"workflow_name": "Open Access Variant Filtering",
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"workflow_short_name": "open-filter",
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"workflow_version": "0.1.0",
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"run_id": "adoring_mercator",
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"session_id": "cd1fcd50-3231-4ce6-9dec-722ed044d970",
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"workflow_version": "0.3.0",
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"run_id": "sleepy_wiles",
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"session_id": "036028b0-f350-433f-8f1b-085b8271f160",
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"inputs": [
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{
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"input_analysis_id": "775eeab5-9cbf-4443-9eea-b59cbf144389",
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"analysis_type": "variant_calling"
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}
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],
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"genome_build": "GRCh38_hla_decoy_ebv"
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"genome_build": "GRCh38_hla_decoy_ebv",
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"genome_annotation": "GENCODE v38"
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},
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"variant_class": "Somatic",
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"info": {
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"origin": "ICGC-25K"
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},
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"variant_class": "Somatic"
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}
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}

‎payload-gen-variant-processing/tests/test-job-1.json‎

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"expected_output": "expected/expected.sanger-wgs.filtered.snv.payload.json",
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"wf_name": "open-access-variant-filtering",
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"wf_short_name": "open-filter",
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"wf_version": "0.1.0",
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"wf_version": "0.3.0",
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"publish_dir": "outdir",
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"cpus": 1,
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"mem": 0.5

‎payload-gen-variant-processing/tests/test-job-2.json‎

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"expected_output": "expected/expected.gatk-mutect2.filtered.snv.payload.json",
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"wf_name": "open-access-variant-filtering",
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"wf_short_name": "open-filter",
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"wf_version": "0.1.0",
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"wf_version": "0.3.0",
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"open": true,
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"publish_dir": "outdir",
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"cpus": 1,

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