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lindaxianglindaxiang
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add test job
1 parent e481d49 commit 26e0af0

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Lines changed: 100 additions & 40 deletions

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

Lines changed: 4 additions & 38 deletions
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@@ -8,8 +8,8 @@
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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": "ridiculous_bhaskara",
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"session_id": "b2c42a90-fb78-4ba3-8a02-0bb02dfbf309",
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"run_id": "deadly_ekeblad",
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"session_id": "e63af1d0-0eaa-42c2-b122-ec6f0bbaa49b",
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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.20211109.star.collectrnaseqmetrics.tgz",
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"fileName": "TEST-PRO.DO001.SA001.rna-seq.20211116.star.collectrnaseqmetrics.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.20211109.star.duplicates_metrics.tgz",
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"fileName": "TEST-PRO.DO001.SA001.rna-seq.20211116.star.duplicates_metrics.tgz",
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"dataType": "Aligned Reads QC"
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},
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{
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"fileSize": 328816,
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"fileMd5sum": "51b57d5b43ee0b188fd0ba2a1b8a64ad",
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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_subtypes": [
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"Read Group Metrics"
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],
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"analysis_tools": [
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"FastQC"
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],
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"files_in_tgz": [
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"TEST-PRO.DO001.SA001.S01L1.e9ea873df5dffc992be7cd3f8c6ee564.lane_fastqc.html",
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"TEST-PRO.DO001.SA001.S01L1.e9ea873df5dffc992be7cd3f8c6ee564.lane_fastqc.zip"
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],
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"metrics": {
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"Basic Statistics": "PASS",
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"Per base sequence quality": "FAIL",
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"Per sequence quality scores": "FAIL",
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"Per base sequence content": "PASS",
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"Per sequence GC content": "WARN",
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"Per base N content": "PASS",
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"Sequence Length Distribution": "PASS",
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"Sequence Duplication Levels": "PASS",
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"Overrepresented sequences": "WARN",
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"Adapter Content": "PASS",
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"read_group_id": "S01L1"
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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.20211109.S01L1.fastqc.tgz",
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"dataType": "Sequencing QC"
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}
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],
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"samples": [

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

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{
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"analysisType": {
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"name": "qc_metrics"
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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": "jovial_ramanujan",
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"session_id": "26009d8f-0cdf-48d6-952d-69e1eb92d2bc",
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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": 328816,
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"fileMd5sum": "51b57d5b43ee0b188fd0ba2a1b8a64ad",
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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_subtypes": [
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"Read Group Metrics"
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],
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"analysis_tools": "FastQC",
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"files_in_tgz": [
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"TEST-PRO.DO001.SA001.S01L1.e9ea873df5dffc992be7cd3f8c6ee564.lane_fastqc.html",
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"TEST-PRO.DO001.SA001.S01L1.e9ea873df5dffc992be7cd3f8c6ee564.lane_fastqc.zip"
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],
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"metrics": {
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"Basic Statistics": "PASS",
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"Per base sequence quality": "FAIL",
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"Per sequence quality scores": "FAIL",
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"Per base sequence content": "PASS",
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"Per sequence GC content": "WARN",
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"Per base N content": "PASS",
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"Sequence Length Distribution": "PASS",
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"Sequence Duplication Levels": "PASS",
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"Overrepresented sequences": "WARN",
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"Adapter Content": "PASS",
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"read_group_id": "S01L1"
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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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"dataType": "Sequencing QC"
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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-2.json‎

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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/TEST-PRO.DO001.SA001.rna-seq.20211012.star.genome_aln.bam.collectrnaseqmetrics.tgz",
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"input/genome.merged.duplicates_metrics.tgz",
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"input/TEST-PRO.DO001.SA001.S01L1.e9ea873df5dffc992be7cd3f8c6ee564.lane.bam.fastqc.tgz"
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"input/genome.merged.duplicates_metrics.tgz"
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],
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"expected_output": "expected/expected.test-job-2.out.json",
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"aligner": "STAR",

‎payload-gen-rna-alignment/tests/test-job-3.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/TEST-PRO.DO001.SA001.S01L1.e9ea873df5dffc992be7cd3f8c6ee564.lane.bam.fastqc.tgz"
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],
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"expected_output": "expected/expected.test-job-3.out.json",
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"aligner": "",
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"analysis_type": "qc_metrics",
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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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