Workflow: portal-workflow.cwl
Fetched 2023-01-09 08:14:49 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- 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_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) |
|
| extra_sample_ids | String[] (Optional) |
Extra sample ids that should be included in case list files |
|
| 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) | ||
| 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) | ||
| 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) |
|
| 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) |
|
| 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) |
|
| 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) |
|
| 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_cna |
full-outer-join.cwl
(CommandLineTool)
|
||
| compile_report |
report.cwl
(CommandLineTool)
|
||
| muts_maf_filter |
maf_filter.cwl
(CommandLineTool)
|
||
| update_cases_all |
updateCaseList.cwl
(CommandLineTool)
|
||
| update_cases_cna |
updateCaseList.cwl
(CommandLineTool)
|
||
| clean_cna_headers |
generate_cBioPortal_file.cwl
(CommandLineTool)
|
||
| generate_cna_data |
copy_number.cwl
(CommandLineTool)
|
||
| concat_hisens_segs |
concat.cwl
(Workflow)
|
||
| generate_cases_cna |
generate_cBioPortal_file.cwl
(CommandLineTool)
|
||
| clean_ascna_headers |
generate_cBioPortal_file.cwl
(CommandLineTool)
|
||
| filter_cbio_fusions |
fusion_filter.cwl
(CommandLineTool)
|
||
| update_cases_cnaseq |
updateCaseList.cwl
(CommandLineTool)
|
||
| concat_cbio_muts_maf |
concat-tables.cwl
(CommandLineTool)
|
||
| generate_cases_cnaseq |
generate_cBioPortal_file.cwl
(CommandLineTool)
|
||
| generate_cbio_meta_cna |
generate_cBioPortal_file.cwl
(CommandLineTool)
|
||
| update_cases_sequenced |
updateCaseList.cwl
(CommandLineTool)
|
||
| generate_cbio_cases_all |
generate_cBioPortal_file.cwl
(CommandLineTool)
|
||
| rename_cbio_hisens_segs |
cp.cwl
(CommandLineTool)
|
||
| update_extra_sample_ids |
portal-workflow.cwl#update_extra_sample_ids/f470479c-9b77-44cd-89b5-3a187fdd9939
(ExpressionTool)
|
||
| generate_cases_sequenced |
generate_cBioPortal_file.cwl
(CommandLineTool)
|
||
| generate_cbio_meta_study |
generate_cBioPortal_file.cwl
(CommandLineTool)
|
||
| replace_illogical_values |
replace.cwl
(CommandLineTool)
|
||
| generate_cbio_fusions_data |
concat.cwl
(Workflow)
|
||
| generate_cbio_meta_fusions |
generate_cBioPortal_file.cwl
(CommandLineTool)
|
||
| generate_meta_cna_segments |
generate_cBioPortal_file.cwl
(CommandLineTool)
|
||
| reduce_sig_figs_hisens_segs |
reduce_sig_figs.cwl
(CommandLineTool)
|
||
| generate_data_clinical_sample |
generate_cBioPortal_file.cwl
(CommandLineTool)
|
||
| generate_meta_clinical_sample |
generate_cBioPortal_file.cwl
(CommandLineTool)
|
||
| generate_data_clinical_patient |
generate_cBioPortal_file.cwl
(CommandLineTool)
|
||
| generate_meta_mutations_extended |
generate_cBioPortal_file.cwl
(CommandLineTool)
|
||
| generate_cbio_clinical_patient_meta |
generate_cBioPortal_file.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| portal_report | File | ||
| portal_muts_file | File | ||
| portal_hisens_segs | File | ||
| portal_case_list_dir | Directory | ||
| portal_cna_data_file | File | ||
| portal_meta_cna_file | File | ||
| portal_cna_ascna_file | File | ||
| portal_meta_study_file | File | ||
| portal_fusions_data_file | File | ||
| portal_meta_fusions_file | File | ||
| portal_meta_cna_segments_file | File | ||
| portal_data_clinical_sample_file | File | ||
| portal_meta_clinical_sample_file | File | ||
| portal_clinical_patient_meta_file | File | ||
| portal_data_clinical_patient_file | File | ||
| portal_meta_mutations_extended_file | File |
https://w3id.org/cwl/view/git/45604eaeea15030c7302941c761464ce392abf74/cwl/portal-workflow.cwl
