Workflow: workflow_with_facets.cwl

Fetched 2023-01-09 09:39:51 GMT

CWL workflow for generating Roslin / Argos post pipeline analysis files and cBioPortal data and metadata files This workflow includes Facets and Facets Suite usages Inputs ------ The following parameters are required: project_id project_pi request_pi project_short_name project_name project_description cancer_type cancer_study_identifier argos_version_string helix_filter_version is_impact extra_pi_groups pairs The following filenames are required: analysis_mutations_filename analysis_gene_cna_filename analysis_sv_filename analysis_segment_cna_filename cbio_segment_data_filename cbio_meta_cna_segments_filename The following filenames have default values and are optional: cbio_mutation_data_filename cbio_cna_data_filename cbio_fusion_data_filename cbio_clinical_patient_data_filename cbio_clinical_sample_data_filename cbio_clinical_sample_meta_filename cbio_clinical_patient_meta_filename cbio_meta_study_filename cbio_meta_cna_filename cbio_meta_fusions_filename cbio_meta_mutations_filename cbio_cases_all_filename cbio_cases_cnaseq_filename cbio_cases_cna_filename cbio_cases_sequenced_filename Output ------ Workflow output should look like this: output ├── analysis │   ├── <project_id>.gene.cna.txt │   ├── <project_id>.muts.maf │   ├── <project_id>.seg.cna.txt │   └── <project_id>.svs.maf ├── facets │ ├── <tumor_id>.<normal_id> (passed) │ │ └── <facets_files> │ └── <tumor_id>.<normal_id> (failed) │ └── <log_files> └── portal ├── case_list │   ├── cases_all.txt │   ├── cases_cnaseq.txt │   ├── cases_cna.txt │   └── cases_sequenced.txt ├── data_clinical_patient.txt ├── data_clinical_sample.txt ├── data_CNA.ascna.txt ├── data_CNA.scna.txt ├── data_CNA.txt ├── data_fusions.txt ├── data_mutations_extended.txt ├── meta_clinical_patient.txt ├── meta_clinical_sample.txt ├── meta_CNA.txt ├── meta_fusions.txt ├── meta_mutations_extended.txt ├── meta_study.txt ├── <project_id>_data_cna_hg19.seg └── <project_id>_meta_cna_hg19_seg.txt

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Inputs

ID Type Title Doc
pairs 8a7c961f10d7e1680d6f052dad84e701[]
is_impact Boolean

whether or not the project is an IMPACT project; should be the value 'True' if so, otherwise any other value means 'False' (IS_IMPACT)
project_id String

unique identifier for the project (PROJ_ID)
project_pi String

principle investigator for the project (PROJ_PI)
request_pi String

principle investigator who requested the project (REQUEST_PI)
cancer_type String

the type of cancer used in the project (CANCER_TYPE)
project_name String

a formal name for the project (PROJ_NAME)
targets_list File
assay_coverage String

genome_coverage value; amount of the genome in bp covered by the assay
extra_cna_files File[] (Optional)

Extra CNA data files to be merged in with the portal CNA data
extra_pi_groups String (Optional)

a list of other groups to be associated with the project in cBioPortal (EXTRA_PI_GROUPS)
tumor_bam_files File[]

Array of tumor bam files. Must match the same order of sample pairs in 'pairs' input field
IMPACT_gene_list File

TSV file with gene labels and corresponding impact assays
extra_sample_ids String[] (Optional)

Extra sample ids that should be included in case list files
normal_bam_files File[]

Array of normal bam files. Must match the same order of sample pairs in 'pairs' input field
data_clinical_file File
known_fusions_file File
project_short_name String

a short name for the project in cBioPortal (PROJ_SHORT_NAME)
project_description String

a description of the project (PROJ_DESC)
sample_summary_file File (Optional)
analysis_sv_filename String

(ANALYSIS_SV_FILE; <project_id>.svs.maf)
argos_version_string String

the version label of Roslin / Argos used to run the project analysis (ARGOS_VERSION_STRING)
helix_filter_version String

the version label of this helix filter repo (HELIX_FILTER_VERSION; git describe --all --long)
microsatellites_file File

Microsatellites list file to use with MSI Sensor
cbio_cna_data_filename String

(CBIO_CNA_DATA_FILENAME)
cbio_meta_cna_filename String

(CBIO_META_CNA_FILE)
mutation_svs_maf_files File[]

analysis_sv_filename (ANALYSIS_SV_FILE; <project_id>.svs.maf): (MAF_DIR)/*.svs.pass.vep.maf
mutation_svs_txt_files File[]

cbio_fusion_data_filename (CBIO_FUSION_DATA_FILENAME; data_fusions.txt): (MAF_DIR)/*.svs.pass.vep.portal.txt
cancer_study_identifier String

a study identifier for the project to use in cBioPortal (CANCER_STUDY_IDENTIFIER)
cbio_cases_all_filename String

(CBIO_CASES_ALL_FILE)
cbio_cases_cna_filename String

(CBIO_CASES_CNA_FILE)
cbio_meta_study_filename String

(CBIO_META_STUDY_FILE)
cbio_fusion_data_filename String

(CBIO_FUSION_DATA_FILENAME)
analysis_gene_cna_filename String

(ANALYSIS_GENE_CNA_FILENAME; <project_id>.gene.cna.txt)
cbio_cases_cnaseq_filename String

(CBIO_CASES_CNASEQ_FILE)
cbio_meta_fusions_filename String

(CBIO_META_FUSIONS_FILE)
cbio_segment_data_filename String

(CBIO_SEGMENT_DATA_FILENAME; <project_id>_data_cna_hg19.seg)
analysis_mutations_filename String

(ANALYSIS_MUTATIONS_FILENAME; <project_id>.muts.maf)
cbio_cna_scna_data_filename String

(CBIO_CNA_SCNA_DATA_FILE)
cbio_mutation_data_filename String

(CBIO_MUTATION_DATA_FILENAME)
cbio_cna_ascna_data_filename String

(CBIO_CNA_ASCNA_DATA_FILE)
cbio_meta_mutations_filename String

(CBIO_META_MUTATIONS_FILE)
analysis_segment_cna_filename String

(ANALYSIS_SEGMENT_CNA_FILE; <project_id>.seg.cna.txt)
cbio_cases_sequenced_filename String

(CBIO_CASES_SEQUENCED_FILE)
cbio_meta_cna_segments_filename String

(cbio_meta_cna_segments_filename; <project_id>_meta_cna_hg19_seg.txt)
analysis_mutations_share_filename String

<project_id>.muts.share.maf)
cbio_clinical_sample_data_filename String

(CBIO_CLINICAL_SAMPLE_DATA_FILENAME)
cbio_clinical_sample_meta_filename String

(CBIO_CLINICAL_SAMPLE_META_FILE)
cbio_clinical_patient_data_filename String

(CBIO_CLINCIAL_PATIENT_DATA_FILENAME)
cbio_clinical_patient_meta_filename String

(CBIO_CLINCAL_PATIENT_META_FILE)

Steps

ID Runs Label Doc
merge_maf
update_cBioPortal_data.cwl (CommandLineTool)
run_facets
facets-workflow.cwl (Workflow)

Workflow for running Facets-suite on a set of tumor normal pairs This workflow scatters over all the pairs in the input JSON to run all samples in parallel Input JSON format ----------------- { \"pairs\": [ { \"tumor_bam\": { \"class\": \"File\", \"path\": \"/test_data/bam/Tumor1.rg.md.abra.printreads.bam\" }, \"normal_bam\": { \"class\": \"File\", \"path\": \"/test_data/bam/Normal1.rg.md.abra.printreads.bam\" }, \"pair_maf\": { \"class\": \"File\", \"path\": \"/test_data/bam/Tumor1.Normal1.maf\" }, \"pair_id\": \"Tumor1.Normal1\" }, { \"tumor_bam\": { \"class\": \"File\", \"path\": \"/test_data/bam/Tumor2.rg.md.abra.printreads.bam\" }, \"normal_bam\": { \"class\": \"File\", \"path\": \"/test_data/bam/Normal2.rg.md.abra.printreads.bam\" }, \"pair_maf\": { \"class\": \"File\", \"path\": \"/test_data/bam/Tumor2.Normal2.maf\" }, \"pair_id\": \"Tumor2.Normal2\" } ] }

Output format ------------- output └── facets-suite ├── Tumor1.Normal1.arm_level.txt ├── Tumor1.Normal1.gene_level.txt ├── Tumor1.Normal1_hisens.ccf.maf ├── Tumor1.Normal1_hisens.rds ├── Tumor1.Normal1_hisens.seg ├── Tumor1.Normal1_purity.rds ├── Tumor1.Normal1_purity.seg ├── Tumor1.Normal1.qc.txt ├── Tumor1.Normal1.snp_pileup.gz ├── Tumor1.Normal1.txt ├── Tumor2.Normal2.arm_level.txt ├── Tumor2.Normal2.gene_level.txt ├── Tumor2.Normal2_hisens.ccf.maf ├── Tumor2.Normal2_hisens.rds ├── Tumor2.Normal2_hisens.seg ├── Tumor2.Normal2_purity.rds ├── Tumor2.Normal2_purity.seg ├── Tumor2.Normal2.qc.txt ├── Tumor2.Normal2.snp_pileup.gz ├── Tumor2.Normal2.txt └── logs ├── success └── failed

run_msi_workflow
msi_workflow.cwl (Workflow)

Workflow to run the MSI analysis on a batch of samples and merge the results back into a single data clinical file

run_tmb_workflow
tmb_workflow.cwl (Workflow)

Workflow to run the TMB analysis on a batch of samples and merge the results back into a single data clinical file

concat_facets_maf
concat-tables.cwl (CommandLineTool)
merge_data_clinical
merge-tables.cwl (CommandLineTool)
run_portal_workflow
portal-workflow.cwl (Workflow)
run_analysis_workflow

Outputs

ID Type Label Doc
facets_dir Directory
portal_dir Directory
analysis_dir Directory
facets_failed_pairs String[]
html json turtle jsonld rdfxml svg png dot zip ro yaml raw
Permalink: https://w3id.org/cwl/view/git/45604eaeea15030c7302941c761464ce392abf74/cwl/workflow_with_facets.cwl