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lindaxianglindaxiang
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Merge pull request #146 from icgc-argo-workflows/payload-gen-rna-alignment@0.1.1
[release]
2 parents 4f452e4 + 46cac4b commit 5cef925

13 files changed

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‎payload-gen-rna-alignment/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 = '0.1.1'
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container = [
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'ghcr.io': 'ghcr.io/icgc-argo-workflows/data-processing-utility-tools.payload-gen-rna-alignment'

‎payload-gen-rna-alignment/main.py‎

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@@ -203,6 +203,7 @@ def get_files_info(file_to_upload, date_str, seq_experiment_analysis_dict, align
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])
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file_info['fileName'] = new_fname
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file_info['fileType'] = new_fname.split('.')[-1].upper()
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file_info['info'] = {
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'data_category': data_type_mapping[file_type][0],

‎payload-gen-rna-alignment/pkg.json‎

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{
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"name": "payload-gen-rna-alignment",
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"version": "0.1.0",
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"version": "0.1.1",
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"description": "payload-gen-rna-alignment",
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"main": "main.nf",
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"deprecated": false,

‎payload-gen-rna-alignment/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 = '0.1.1'
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container = [
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'ghcr.io': 'ghcr.io/icgc-argo-workflows/data-processing-utility-tools.payload-gen-rna-alignment'

‎payload-gen-rna-alignment/tests/expected/expected.test-job-1.out.json‎

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"workflow_version": "0.1.0",
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"genome_build": "GRCh38_hla_decoy_ebv",
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"genome_annotation": "GENCODE v38",
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"run_id": "insane_hugle",
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"session_id": "67ccf9ba-915e-4dda-ac5c-975fd1ff0509",
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"run_id": "admiring_minsky",
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"session_id": "1b279d9a-2ed3-49e7-8bff-1ee0255a1245",
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"inputs": [
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{
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"analysis_type": "sequencing_experiment",
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"STAR"
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]
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},
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"fileName": "TEST-PRO.DO001.SA001.rna-seq.20211109.star.genome_aln.cram",
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"fileName": "TEST-PRO.DO001.SA001.rna-seq.20211207.star.genome_aln.cram",
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"fileType": "CRAM",
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"dataType": "Aligned Reads"
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},
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{
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"STAR"
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]
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},
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"fileName": "TEST-PRO.DO001.SA001.rna-seq.20211109.star.genome_aln.cram.crai",
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"fileName": "TEST-PRO.DO001.SA001.rna-seq.20211207.star.genome_aln.cram.crai",
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"fileType": "CRAI",
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"dataType": "Aligned Reads Index"
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}
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],

‎payload-gen-rna-alignment/tests/expected/expected.test-job-2.out.json‎

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"workflow_version": "0.1.0",
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"genome_build": "GRCh38_hla_decoy_ebv",
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"genome_annotation": "GENCODE v38",
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"run_id": "deadly_ekeblad",
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"session_id": "e63af1d0-0eaa-42c2-b122-ec6f0bbaa49b",
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"run_id": "focused_shirley",
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"session_id": "09c96e0c-b63f-450a-b5aa-97ba0a4aa4a6",
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"inputs": [
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{
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"analysis_type": "sequencing_experiment",
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},
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"description": "RNA alignment metrics for a SAM or BAM file."
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},
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"fileName": "TEST-PRO.DO001.SA001.rna-seq.20211116.star.collectrnaseqmetrics.tgz",
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"fileName": "TEST-PRO.DO001.SA001.rna-seq.20211207.star.collectrnaseqmetrics.tgz",
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"fileType": "TGZ",
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"dataType": "Aligned Reads QC"
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},
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{
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]
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}
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},
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"fileName": "TEST-PRO.DO001.SA001.rna-seq.20211116.star.duplicates_metrics.tgz",
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"fileName": "TEST-PRO.DO001.SA001.rna-seq.20211207.star.duplicates_metrics.tgz",
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"fileType": "TGZ",
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"dataType": "Aligned Reads QC"
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}
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],

‎payload-gen-rna-alignment/tests/expected/expected.test-job-3.out.json‎

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"workflow_version": "0.1.0",
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"genome_build": "GRCh38_hla_decoy_ebv",
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"genome_annotation": "GENCODE v38",
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"run_id": "jovial_ramanujan",
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"session_id": "26009d8f-0cdf-48d6-952d-69e1eb92d2bc",
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"run_id": "sick_hilbert",
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"session_id": "575a320a-f228-48d7-a311-b8a314d66e6b",
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"inputs": [
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{
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"analysis_type": "sequencing_experiment",
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},
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"description": "High level sequencing reads QC metrics generated by FastQC."
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},
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"fileName": "TEST-PRO.DO001.SA001.rna-seq.20211116.S01L1.fastqc.tgz",
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"fileName": "TEST-PRO.DO001.SA001.rna-seq.20211207.S01L1.fastqc.tgz",
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"fileType": "TGZ",
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"dataType": "Sequencing QC"
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}
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],

‎payload-gen-rna-alignment/tests/expected/expected.test-job-4.out.json‎

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{
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"analysisType": {
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"name": "supplement"
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},
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"studyId": "TEST-PRO",
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"workflow": {
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"workflow_name": "RNA Seq Alignment",
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"workflow_version": "0.1.0",
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"genome_build": "GRCh38_hla_decoy_ebv",
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"genome_annotation": "GENCODE v38",
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"run_id": "peaceful_lamarr",
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"session_id": "69bb68a1-8e00-4fca-8919-dd476f8deb53",
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"inputs": [
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{
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"analysis_type": "sequencing_experiment",
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"input_analysis_id": null
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}
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]
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},
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"files": [
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{
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"fileSize": 1985,
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"fileMd5sum": "ef7925492346751fe88557acbffef877",
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"fileAccess": "controlled",
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"info": {
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"data_category": "Supplement",
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"data_subtypes": [
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null
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],
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"analysis_tools": [
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"HiSAT2"
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],
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"files_in_tgz": [
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"SA001_RG_S01L1_metrics.txt",
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"SA001_RG_S01L2_metrics.txt",
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"SA001_RG_S01L1_summary.txt",
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"SA001_RG_S01L2_summary.txt",
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"align.log"
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]
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},
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"fileName": "TEST-PRO.DO001.SA001.rna-seq.20211207.hisat2.supplement.tgz",
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"fileType": "TGZ",
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"dataType": "Running Logs"
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}
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],
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"samples": [
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{
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"submitterSampleId": "donor1_sample1_id",
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"matchedNormalSubmitterSampleId": "sample1_normal",
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"sampleType": "RNA",
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"specimen": {
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"submitterSpecimenId": "donor1_sample1",
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"tumourNormalDesignation": "tumor",
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"specimenTissueSource": "simulated",
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"specimenType": "simulated"
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},
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"donor": {
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"submitterDonorId": "donor1",
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"gender": "male"
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}
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}
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],
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"experiment": {
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"submitter_sequencing_experiment_id": "TEST_EXP",
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"sequencing_center": "SIM",
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"platform": "ILLUMINA",
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"platform_model": "Polyester",
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"experimental_strategy": "RNA-Seq",
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"sequencing_date": "2021-04-21"
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}
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}

‎payload-gen-rna-alignment/tests/expected/expected.test-job-5.out.json‎

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{
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"analysisType": {
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"name": "splice_junctions"
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},
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"studyId": "TEST-PRO",
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"workflow": {
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"workflow_name": "RNA Seq Alignment",
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"workflow_version": "0.1.0",
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"genome_build": "GRCh38_hla_decoy_ebv",
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"genome_annotation": "GENCODE v38",
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"run_id": "hopeful_noyce",
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"session_id": "2702543c-1cb1-47e5-b2c6-5f362f2ee269",
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"inputs": [
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{
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"analysis_type": "sequencing_experiment",
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"input_analysis_id": null
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}
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]
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},
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"files": [
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{
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"fileSize": 371,
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"fileMd5sum": "14bc8619e7463a4c01f957729dae174e",
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"fileAccess": "controlled",
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"info": {
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"data_category": "Transcriptome Profiling",
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"data_subtypes": [
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null
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],
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"analysis_tools": [
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"HiSAT2"
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]
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},
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"fileName": "TEST-PRO.DO001.SA001.rna-seq.20211207.hisat2.splice_junctions.txt",
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"fileType": "TXT",
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"dataType": "Splice Junctions"
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}
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],
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"samples": [
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{
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"submitterSampleId": "donor1_sample1_id",
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"matchedNormalSubmitterSampleId": "sample1_normal",
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"sampleType": "RNA",
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"specimen": {
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"submitterSpecimenId": "donor1_sample1",
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"tumourNormalDesignation": "tumor",
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"specimenTissueSource": "simulated",
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"specimenType": "simulated"
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},
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"donor": {
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"submitterDonorId": "donor1",
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"gender": "male"
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}
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}
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],
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"experiment": {
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"submitter_sequencing_experiment_id": "TEST_EXP",
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"sequencing_center": "SIM",
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"platform": "ILLUMINA",
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"platform_model": "Polyester",
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"experimental_strategy": "RNA-Seq",
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"sequencing_date": "2021-04-21"
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}
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}

‎payload-gen-rna-alignment/tests/test-job-4.json‎

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{
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"seq_experiment_analysis": "input/s3.881fe6cf-8c80-4c7b-9f4d-b8dac9601d01.sequencing_experiment.payload.json",
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"files_to_upload": [
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"input/SA001.hisat2.all_logs.supplement.tar.gz"
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],
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"expected_output": "expected/expected.test-job-4.out.json",
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"aligner": "hisat2",
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"analysis_type": "supplement",
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"genome_annotation": "GENCODE v38",
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"genome_build": "GRCh38_hla_decoy_ebv",
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"wf_name": "rna-seq-alignment",
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"wf_version": "0.1.0",
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"publish_dir": "outdir",
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"cpus": 1,
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"mem": 0.5
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}

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