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lindaxianglindaxiang
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Merge pull request #164 from icgc-argo-workflows/payload-gen-rna-alignment@0.2.0
[release]
2 parents a1a16ab + c10612e commit d23e5d2

17 files changed

Lines changed: 123 additions & 27 deletions

‎payload-gen-rna-alignment/main.nf‎

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@@ -24,7 +24,7 @@
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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
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version = '0.1.3'
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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.payload-gen-rna-alignment'
@@ -55,7 +55,7 @@ params.genome_build = ""
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process payloadGenRnaAlignment {
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container "${params.container ?: container[params.container_registry ?: default_container_registry]}:${params.container_version ?: version}"
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publishDir "${params.publish_dir}/${task.process.replaceAll(':', '_')}", mode: "copy", enabled: params.publish_dir
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publishDir "${params.publish_dir}/${task.process.replaceAll(':', '_')}", mode: "copy", enabled: params.publish_dir ? true : false
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cpus params.cpus
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memory "${params.mem} GB"

‎payload-gen-rna-alignment/main.py‎

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@@ -150,7 +150,7 @@ def get_files_info(file_to_upload, date_str, seq_experiment_analysis_dict, align
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submitter_rg_id = None
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if re.match(r'^genome.merged.+?(cram|cram\.crai|bam|bam\.bai)$', file_to_upload):
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file_type = 'genome_aln'
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elif re.match(r'^transcriptome.merged.+?(cram|cram\.crai|bam|bam\.bai)$', file_to_upload):
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elif re.match(r'.+?_Aligned\.toTranscriptome\.out\.bam$', file_to_upload):
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file_type = 'transcriptome_aln'
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elif re.match(r'^chimeric.merged.+?(cram|cram\.crai|bam|bam\.bai)$', file_to_upload):
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file_type = 'chimeric_aln'
@@ -282,8 +282,8 @@ def main():
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help="Input analysis for sequencing experiment", type=str)
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parser.add_argument("-t", "--analysis_type", dest="analysis_type", required=True, help="Specify analysis_type")
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parser.add_argument("-l", "--aligner", dest="aligner", default=None, help="Provide RNA-Seq aligner if files_to_upload are generated from alignment results. Default=None")
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parser.add_argument("-g", "--genome_annotation", dest="genome_annotation", default="GENCODE v38", help="RNA-Seq alignment genome annotation")
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parser.add_argument("-b", "--genome_build", dest="genome_build", default="GRCh38_hla_decoy_ebv", help="RNA-Seq alignment genome build")
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parser.add_argument("-g", "--genome_annotation", dest="genome_annotation", default="GENCODE v40", help="RNA-Seq alignment genome annotation")
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parser.add_argument("-b", "--genome_build", dest="genome_build", default="GRCh38_Verily_v1", help="RNA-Seq alignment genome build")
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parser.add_argument("-w", "--wf_name", dest="wf_name", required=True, help="Workflow name")
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parser.add_argument("-v", "--wf_version", dest="wf_version", required=True, help="Workflow version")
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parser.add_argument("-r", "--wf_run", dest="wf_run", required=True, help="Workflow run ID")

‎payload-gen-rna-alignment/pkg.json‎

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@@ -1,6 +1,6 @@
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{
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"name": "payload-gen-rna-alignment",
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"version": "0.1.3",
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"version": "0.2.0",
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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 = '0.1.3'
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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.payload-gen-rna-alignment'

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

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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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"genome_build": "GRCh38_Verily_v1",
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"genome_annotation": "GENCODE v40",
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"run_id": "admiring_minsky",
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"session_id": "1b279d9a-2ed3-49e7-8bff-1ee0255a1245",
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"inputs": [

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

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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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"genome_build": "GRCh38_Verily_v1",
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"genome_annotation": "GENCODE v40",
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"run_id": "focused_shirley",
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"session_id": "09c96e0c-b63f-450a-b5aa-97ba0a4aa4a6",
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"inputs": [

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

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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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"genome_build": "GRCh38_Verily_v1",
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"genome_annotation": "GENCODE v40",
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"run_id": "lonely_thompson",
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"session_id": "6fb88d81-ad07-4c1b-bcfa-51e133e836fe",
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"inputs": [

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

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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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"genome_build": "GRCh38_Verily_v1",
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"genome_annotation": "GENCODE v40",
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"run_id": "peaceful_lamarr",
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"session_id": "69bb68a1-8e00-4fca-8919-dd476f8deb53",
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"inputs": [

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

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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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"genome_build": "GRCh38_Verily_v1",
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"genome_annotation": "GENCODE v40",
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"run_id": "hopeful_noyce",
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"session_id": "2702543c-1cb1-47e5-b2c6-5f362f2ee269",
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"inputs": [

‎payload-gen-rna-alignment/tests/expected/expected.test-job-6.out.json‎

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{
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"analysisType": {
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"name": "sequencing_alignment"
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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": "0.2.0",
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"genome_build": "GRCh38_Verily_v1",
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"genome_annotation": "GENCODE v40",
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"run_id": "pedantic_brenner",
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"session_id": "b65970c3-192f-40dc-99f1-aedba8b987fe",
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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": 51177,
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"fileMd5sum": "f1c42eb0bc3aa8dc83cc3acac8632484",
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"fileAccess": "controlled",
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"info": {
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"data_category": "Sequencing Reads",
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"data_subtypes": [
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"Transcriptome Alignment"
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],
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"analysis_tools": [
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"STAR"
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]
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},
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"fileName": "TEST-PRO.DO001.SA001.rna-seq.20221118.star.transcriptome_aln.bam",
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"fileType": "BAM",
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"dataType": "Aligned Reads"
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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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"read_group_count": 1,
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"read_groups": [
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{
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"submitter_read_group_id": "S01L1",
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"read_group_id_in_bam": null,
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"platform_unit": "sim01",
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"is_paired_end": true,
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"file_r1": "sample_01_L1_1.fastq.gz",
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"file_r2": "sample_01_L1_2.fastq.gz",
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"read_length_r1": 100,
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"read_length_r2": 100,
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"insert_size": 250,
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"sample_barcode": null,
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"library_name": "sim01"
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}
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]
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}

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