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Merge pull request #148 from icgc-argo-workflows/json-parser@0.2.0
[release]
2 parents 337a550 + ecb2cad commit 5dec0de

6 files changed

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‎json-parser/main.nf‎

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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
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version = '0.1.0' // package version
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version = '0.2.0'
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container = [
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'ghcr.io': 'ghcr.io/icgc-argo-workflows/data-processing-utility-tools.json-parser'

‎json-parser/pkg.json‎

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{
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"name": "json-parser",
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"version": "0.1.0",
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"version": "0.2.0",
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"description": "tool to parse JSON metadata",
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"main": "main.nf",
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"deprecated": false,

‎json-parser/tests/checker.nf‎

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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
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version = '0.1.0' // package version
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version = '0.2.0'
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container = [
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'ghcr.io': 'ghcr.io/icgc-argo-workflows/data-processing-utility-tools.json-parser'

‎json-parser/tests/data‎

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This file was deleted.

‎json-parser/tests/data/40054341-119d-492e-8543-41119dc92ea1.sequencing_experiment.4.analysis.json‎

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"analysisId": "40054341-119d-492e-8543-41119dc92ea1",
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"studyId": "TEST-PRO",
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"info": {
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"sampleId": "SAbc064f25adab65a4c75a539e5e2b8d48",
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],
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"analysisType": {
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"name": "sequencing_experiment",
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"version": 4
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"experiment": {
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"platform": "ILLUMINA",
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"platform_model": "HiSeq 2000",
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"sequencing_date": "2014-12-12",
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"library_strategy": "WGS",
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"sequencing_center": "EXT",
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"submitter_sequencing_experiment_id": "TEST_EXP",
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},
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"library_name": "Pond-147580",
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"is_paired_end": true,
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"platform_unit": "74_8a",
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"read_length_r1": 150,
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"submitter_read_group_id": "C0HVY.2"
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{
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"file_r1": "test_rg_3.bam",
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"insert_size": 298,
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"library_name": "Pond-147580",
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"is_paired_end": true,
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"platform_unit": "74_8b",
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"read_length_r1": 150,
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"sample_barcode": null,
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"submitter_read_group_id": "D0RE2.1"
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},
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{
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"file_r1": "test_rg_3.bam",
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"file_r2": "test_rg_3.bam",
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"insert_size": 298,
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"library_name": "Pond-147580",
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"is_paired_end": true,
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"submitter_read_group_id": "D0RH0.2"
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"read_group_count": 3
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}

‎json-parser/tests/data/89176bbc-ffca-4d73-984a-4a92ed931a98.sequencing_experiment.4.analysis.json‎

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{
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"analysisId": "40054341-119d-492e-8543-41119dc92ea1",
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"studyId": "TEST-PRO",
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"analysisState": "UNPUBLISHED",
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"samples": [
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{
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"sampleId": "SAbc064f25adab65a4c75a539e5e2b8d48",
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"specimenId": "SPea740f45bacdf68583eeb9183e8bb57a",
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"submitterSampleId": "HCC1143_BAM_INPUT",
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"matchedNormalSubmitterSampleId": null,
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"sampleType": "Total DNA",
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"specimen": {
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"specimenId": "SPea740f45bacdf68583eeb9183e8bb57a",
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"donorId": "DO1d5c9010f8ddcc4b7be855ddaa9cdd3c",
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"submitterSpecimenId": "TEST_EXP",
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"tumourNormalDesignation": "Tumour"
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},
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"donor": {
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"donorId": "DO1d5c9010f8ddcc4b7be855ddaa9cdd3c",
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"studyId": "TEST-PRO",
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"gender": "Female",
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"submitterDonorId": "internal_donor_123456789-00"
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}
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}
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"files": [
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{
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"objectId": "69c0148d-68a0-5acb-8925-14e7eb4a1725",
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"studyId": "TEST-PRO",
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"analysisId": "40054341-119d-492e-8543-41119dc92ea1",
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"fileName": "test_rg_3.bam",
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"fileSize": 14911,
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"fileType": "BAM",
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"fileMd5sum": "178f97f7b1ca8bfc28fd5586bdd56799",
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"fileAccess": "controlled",
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"dataType": "UnalignedReads"
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}
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],
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"analysisType": {
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"name": "sequencing_experiment",
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"version": 4
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},
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"experiment": {
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"platform": "ILLUMINA",
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"platform_model": "HiSeq 2000",
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"sequencing_date": "2014-12-12",
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"library_strategy": "WGS",
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"sequencing_center": "EXT",
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"submitter_sequencing_experiment_id": "TEST_EXP"
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},
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"read_groups": [
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{
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"file_r1": "test_rg_3.bam",
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"file_r2": "test_rg_3.bam",
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"insert_size": 298,
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"library_name": "Pond-147580",
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"read_group_id_in_bam": "C0HVY.2",
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"submitter_read_group_id": "C0HVY:2"
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{
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"file_r1": "test_rg_3.bam",
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"submitter_read_group_id": "C0HVY_2"
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},
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{
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"file_r1": "test_rg_3.bam",
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"file_r2": "test_rg_3.bam",
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"insert_size": 298,
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"library_name": "Pond-147580",
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"is_paired_end": false,
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"platform_unit": "74_8c",
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"read_length_r1": 150,
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"read_length_r2": 150,
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"sample_barcode": null,
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"read_group_id_in_bam": "D0RH0.2",
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"submitter_read_group_id": "C0HVY_2_1"
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}
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],
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"read_group_count": 3
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}

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