Workflow: workflow.cwl
Fetched 2023-01-09 07:41:18 GMT
Verified with cwltool version 3.1.20221201130942
CWL workflow for generating Roslin / Argos post pipeline analysis files and cBioPortal data and metadata files 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 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 └── 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
- Selected
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- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| 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 | ||
| extra_pi_groups | String (Optional) |
a list of other groups to be associated with the project in cBioPortal (EXTRA_PI_GROUPS) |
|
| IMPACT_gene_list | File |
TSV file with gene labels and corresponding impact assays |
|
| data_clinical_file | File | ||
| known_fusions_file | File | ||
| mutation_maf_files | File[] |
analysis_mutations_filename (ANALYSIS_MUTATIONS_FILENAME) cbio_mutation_data_filename (CBIO_MUTATION_DATA_FILENAME): (MAF_DIR)/*.muts.maf |
|
| 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) |
|
| cbio_cna_data_filename | String |
(CBIO_CNA_DATA_FILENAME) |
|
| cbio_meta_cna_filename | String |
(CBIO_META_CNA_FILE) |
|
| facets_suite_txt_files | File[] (Optional) |
Facets Suite .txt files for all samples in the request |
|
| 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) |
|
| facets_hisens_seg_files | File[] |
cbio_segment_data_filename (CBIO_SEGMENT_DATA_FILENAME; <project_id>_data_cna_hg19.seg) analysis_segment_cna_filename (ANALYSIS_SEGMENT_CNA_FILE; <project_id>.seg.cna.txt): (FACETS_DIR)/*_hisens.seg |
|
| cbio_meta_study_filename | String |
(CBIO_META_STUDY_FILE) |
|
| facets_hisens_cncf_files | File[] |
cbio_cna_data_filename (CBIO_CNA_DATA_FILENAME; data_CNA.txt) analysis_gene_cna_filename (ANALYSIS_GENE_CNA_FILENAME; <project_id>.gene.cna.txt): (FACETS_DIR)/*_hisens.cncf.txt |
|
| 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 |
|---|---|---|---|
| run_portal_workflow |
portal-workflow.cwl
(Workflow)
|
||
| run_analysis_workflow |
analysis-workflow.cwl
(Workflow)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| portal_dir | Directory | ||
| analysis_dir | Directory |
https://w3id.org/cwl/view/git/5cad957fec135aa55ca8d588372db0557ca1cad5/cwl/workflow.cwl
