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junjun-zhangjunjun-zhang
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Merge pull request #122 from icgc-argo/payload-gen-variant-calling@0.5.0
[release]
2 parents 1066cd6 + 4ad9464 commit ac22a9f

8 files changed

Lines changed: 55 additions & 32 deletions

‎payload-gen-variant-calling/main.nf‎

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@@ -25,7 +25,7 @@
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/* this block is auto-generated based on info from pkg.json where */
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/* changes can be made if needed, do NOT modify this block manually */
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nextflow.enable.dsl = 2
28-
version = '0.4.0' // package version
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version = '0.5.0'
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container = [
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'ghcr.io': 'ghcr.io/icgc-argo/data-processing-utility-tools.payload-gen-variant-calling'

‎payload-gen-variant-calling/main.py‎

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@@ -33,21 +33,21 @@
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variant_type_to_data_type_etc = {
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'snv': ['Simple Nucleotide Variation', ['Raw SNV Calls', None], ['CaVEMan'], ['GATK:Mutect2']], # dataCategory, [dataType, data_subtype], analysis_tools
36+
'snv': ['Simple Nucleotide Variation', ['Raw SNV Calls', None], ['CaVEMan'], ['GATK:Mutect2']], # dataCategory, [dataType, data_subtypes], analysis_tools
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'indel': ['Simple Nucleotide Variation', ['Raw InDel Calls', None], ['Pindel'], ['GATK:Mutect2']],
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'cnv': ['Copy Number Variation', ['Raw CNV Calls', None], ['ASCAT']],
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'sv': ['Structural Variation', ['Raw SV Calls', None], ['BRASS']],
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'caveman-supplement': ['Simple Nucleotide Variation', ['SNV Supplement', None], ['CaVEMan']],
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'pindel-supplement': ['Simple Nucleotide Variation', ['InDel Supplement', None], ['Pindel']],
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'ascat-supplement': ['Copy Number Variation', ['CNV Supplement', None], ['ASCAT']],
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'brass-supplement': ['Structural Variation', ['SV Supplement', None], ['BRASS']],
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'timings-supplement': ['Quality Control Metrics', ['Analysis QC', 'Runtime Stats'], None, None],
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'bas_metrics': ['Quality Control Metrics', ['Aligned Reads QC', 'Alignment Metrics'], ['Sanger:bam_stats']],
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'contamination_metrics': ['Quality Control Metrics', ['Analysis QC', 'Cross Sample Contamination'], ['Sanger:verifyBamHomChk'], ['GATK:CalculateContamination']],
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'ascat_metrics': ['Quality Control Metrics', ['Analysis QC', 'Ploidy and Purity Estimation'], ['ASCAT']],
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'genotyped_gender_metrics': ['Quality Control Metrics', ['Analysis QC', 'Genotyping Stats'], ['Sanger:compareBamGenotypes']],
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'mutect_filtering_metrics': ['Quality Control Metrics', ['Analysis QC', 'Variant Filtering Stats'], [], ['GATK:FilterMutectCalls']],
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'mutect_callable_metrics': ['Quality Control Metrics', ['Analysis QC', 'Variant Callable Stats'], [], ['GATK:Mutect2']],
44+
'timings-supplement': ['Quality Control Metrics', ['Analysis QC', ['Runtime Stats']], None, None],
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'bas_metrics': ['Quality Control Metrics', ['Aligned Reads QC', ['Alignment Metrics']], ['Sanger:bam_stats']],
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'contamination_metrics': ['Quality Control Metrics', ['Analysis QC', ['Cross Sample Contamination']], ['Sanger:verifyBamHomChk'], ['GATK:CalculateContamination']],
47+
'ascat_metrics': ['Quality Control Metrics', ['Analysis QC', ['Ploidy', 'Tumour Purity']], ['ASCAT']],
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'genotyped_gender_metrics': ['Quality Control Metrics', ['Analysis QC', ['Genotyping Stats']], ['Sanger:compareBamGenotypes']],
49+
'mutect_filtering_metrics': ['Quality Control Metrics', ['Analysis QC', ['Variant Filtering Stats']], [], ['GATK:FilterMutectCalls']],
50+
'mutect_callable_metrics': ['Quality Control Metrics', ['Analysis QC', ['Variant Callable Stats']], [], ['GATK:Mutect2']],
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}
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workflow_full_name = {
@@ -151,22 +151,22 @@ def get_files_info(file_to_upload, wf_short_name, wf_version, somatic_or_germli
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file_info['info'] = {
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'data_category': variant_type_to_data_type_etc[variant_type][0],
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'data_subtype': None
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'data_subtypes': None
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}
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extra_info = {}
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if new_fname.endswith('.vcf.gz'):
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file_info['dataType'] = variant_type_to_data_type_etc[variant_type][1][0]
160-
file_info['info']['data_subtype'] = variant_type_to_data_type_etc[variant_type][1][1]
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file_info['info']['data_subtypes'] = variant_type_to_data_type_etc[variant_type][1][1]
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elif new_fname.endswith('.vcf.gz.tbi'):
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file_info['dataType'] = 'VCF Index'
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elif new_fname.endswith('.tgz'):
164164
if new_fname.endswith('-supplement.tgz'):
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file_info['dataType'] = variant_type_to_data_type_etc[variant_type][1][0]
166-
file_info['info']['data_subtype'] = variant_type_to_data_type_etc[variant_type][1][1]
166+
file_info['info']['data_subtypes'] = variant_type_to_data_type_etc[variant_type][1][1]
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elif new_fname.endswith('_metrics.tgz'):
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file_info['dataType'] = variant_type_to_data_type_etc[variant_type][1][0]
169-
file_info['info']['data_subtype'] = variant_type_to_data_type_etc[variant_type][1][1]
169+
file_info['info']['data_subtypes'] = variant_type_to_data_type_etc[variant_type][1][1]
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else:
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sys.exit('Error: unknown file type "%s"' % file_to_upload)
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‎payload-gen-variant-calling/pkg.json‎

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{
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"name": "payload-gen-variant-calling",
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"version": "0.4.0",
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"version": "0.5.0",
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"description": "A tool to generate SONG payloads for variant calling workflows",
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"main": "main.nf",
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"deprecated": false,
@@ -33,4 +33,4 @@
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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"
36-
}
36+
}

‎tests/data/1a7df8db-cb54-43e1-952f-3c458a14800a.variant_calling.payload.json‎

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"fileAccess": "controlled",
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"info": {
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"data_category": "Simple Nucleotide Variation",
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"data_subtype": null,
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"data_subtypes": null,
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"analysis_tools": [
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"CaVEMan"
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]
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"fileAccess": "controlled",
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"info": {
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"data_category": "Simple Nucleotide Variation",
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"data_subtype": null,
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"data_subtypes": null,
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"analysis_tools": [
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"CaVEMan"
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]

‎tests/data/66f84b1e-dad1-4981-916e-07e62ff53410.variant_calling_supplement.payload.json‎

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"fileAccess": "controlled",
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"info": {
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"data_category": "Quality Control Metrics",
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"data_subtype": "Runtime Stats",
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"data_subtypes": [
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"Runtime Stats"
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],
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"analysis_tools": null,
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"description": "Files contain timing information for different processing steps",
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"files": [
@@ -66,7 +68,7 @@
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"fileAccess": "controlled",
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"info": {
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"data_category": "Simple Nucleotide Variation",
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"data_subtype": null,
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"data_subtypes": null,
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"analysis_tools": [
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"CaVEMan"
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],
@@ -98,7 +100,7 @@
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"fileAccess": "controlled",
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"info": {
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"data_category": "Simple Nucleotide Variation",
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"data_subtype": null,
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"data_subtypes": null,
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"analysis_tools": [
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"Pindel"
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],

‎tests/data/735a4c34-c928-4f03-957b-fe808df68f63.qc_metrics.payload.json‎

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"fileAccess": "controlled",
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"info": {
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"data_category": "Quality Control Metrics",
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"data_subtype": "Cross Sample Contamination",
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"data_subtypes": [
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"Cross Sample Contamination"
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],
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"analysis_tools": [
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"GATK:CalculateContamination"
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],
@@ -61,7 +63,9 @@
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"fileAccess": "controlled",
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"info": {
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"data_category": "Quality Control Metrics",
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"data_subtype": "Cross Sample Contamination",
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"data_subtypes": [
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"Cross Sample Contamination"
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],
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"analysis_tools": [
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"GATK:CalculateContamination"
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],
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"fileAccess": "controlled",
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"info": {
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"data_category": "Quality Control Metrics",
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"data_subtype": "Variant Filtering Stats",
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"data_subtypes": [
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"Variant Filtering Stats"
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],
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"analysis_tools": [
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"GATK:FilterMutectCalls"
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],
@@ -162,7 +168,9 @@
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"fileAccess": "controlled",
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"info": {
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"data_category": "Quality Control Metrics",
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"data_subtype": "Variant Callable Stats",
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"data_subtypes": [
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"Variant Callable Stats"
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],
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"analysis_tools": [
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"GATK:Mutect2"
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],

‎tests/data/d354c4b2-db32-41f0-973f-db1306a99a84.qc_metrics.payload.json‎

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"fileAccess": "controlled",
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"info": {
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"data_category": "Quality Control Metrics",
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"data_subtype": "Cross Sample Contamination",
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"data_subtypes": [
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"Cross Sample Contamination"
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],
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"analysis_tools": [
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"Sanger:verifyBamHomChk"
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],
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"fileAccess": "controlled",
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"info": {
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"data_category": "Quality Control Metrics",
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"data_subtype": "Cross Sample Contamination",
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"data_subtypes": [
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"Cross Sample Contamination"
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],
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"analysis_tools": [
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"Sanger:verifyBamHomChk"
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],
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"fileAccess": "controlled",
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"info": {
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"data_category": "Quality Control Metrics",
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"data_subtype": "Alignment Metrics",
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"data_subtypes": [
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"Alignment Metrics"
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],
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"analysis_tools": [
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"Sanger:bam_stats"
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],
@@ -115,7 +121,9 @@
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"fileAccess": "controlled",
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"info": {
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"data_category": "Quality Control Metrics",
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"data_subtype": "Alignment Metrics",
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"data_subtypes": [
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"Alignment Metrics"
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],
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"analysis_tools": [
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"Sanger:bam_stats"
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],
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"fileAccess": "controlled",
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"info": {
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"data_category": "Quality Control Metrics",
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"data_subtype": "Ploidy and Purity Estimation",
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"data_subtypes": [
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"Ploidy",
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"Tumour Purity"
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],
138149
"analysis_tools": [
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"ASCAT"
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],
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"fileAccess": "controlled",
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"info": {
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"data_category": "Quality Control Metrics",
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"data_subtype": "Genotyping Stats",
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"data_subtypes": [
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"Genotyping Stats"
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],
166179
"analysis_tools": [
167180
"Sanger:compareBamGenotypes"
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],

‎tests/data/f7ca0bd4-53a7-4663-b7b6-1b3d414e0018.variant_calling.payload.json‎

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"fileAccess": "controlled",
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"info": {
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"data_category": "Simple Nucleotide Variation",
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"data_subtype": null,
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"data_subtypes": null,
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"analysis_tools": [
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"GATK:Mutect2"
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]
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"fileAccess": "controlled",
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"info": {
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"data_category": "Simple Nucleotide Variation",
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"data_subtype": null,
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"data_subtypes": null,
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"analysis_tools": [
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"GATK:Mutect2"
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]

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