Workflow: portal-workflow.cwl
Fetched 2024-11-22 10:51:23 GMT
Verified with cwltool version 3.1.20230201224320
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- Default Values
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- Inputs/Outputs
Unknown workflow license, check
source repository.
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' |
|
| msi_files | File[] |
msi.tsv files |
|
| tmb_files | File[] |
*.tmb.tsv files |
|
| project_id | String |
unique identifier for the project |
|
| project_pi | String |
principle investigator for the project |
|
| request_pi | String |
principle investigator who requested the project |
|
| cancer_type | String |
the type of cancer used in the project |
|
| project_name | String |
a formal name for the project |
|
| 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_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[] |
*.muts.maf |
|
| project_short_name | String |
a short name for the project in cBioPortal |
|
| project_description | String |
a description of the project |
|
| sample_summary_file | File (Optional) | ||
| argos_version_string | String |
the version label of Roslin / Argos used to run the project analysis |
|
| helix_filter_version | String |
the version label of this helix filter repo (git describe --all --long) |
|
| cbio_meta_sv_filename | String | ||
| cbio_sv_data_filename | String | ||
| cbio_cna_data_filename | String | ||
| cbio_meta_cna_filename | String | ||
| facets_suite_txt_files | File[] (Optional) | ||
| mutation_svs_txt_files | File[] |
*.svs.pass.vep.portal.txt |
|
| cancer_study_identifier | String |
a study identifier for the project to use in cBioPortal |
|
| cbio_cases_all_filename | String | ||
| cbio_cases_cna_filename | String | ||
| facets_hisens_seg_files | File[] |
*_hisens.seg |
|
| cbio_meta_study_filename | String | ||
| facets_hisens_cncf_files | File[] |
*_hisens.cncf.txt |
|
| cbio_fusion_data_filename | String | ||
| cbio_cases_cnaseq_filename | String | ||
| cbio_meta_fusions_filename | String | ||
| cbio_segment_data_filename | String |
<project_id>_data_cna_hg19.seg) |
|
| cbio_cna_scna_data_filename | String | ||
| cbio_mutation_data_filename | String | ||
| cbio_cna_ascna_data_filename | String | ||
| cbio_meta_mutations_filename | String | ||
| cbio_cases_sequenced_filename | String | ||
| cbio_meta_cna_segments_filename | String |
<project_id>_meta_cna_hg19_seg.txt) |
|
| cbio_clinical_sample_data_filename | String | ||
| cbio_clinical_sample_meta_filename | String | ||
| cbio_clinical_patient_data_filename | String | ||
| cbio_clinical_patient_meta_filename | String |
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)
|
||
| concat_msi_tables |
concat-tables.cwl
(CommandLineTool)
|
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| concat_tmb_tables |
concat-tables.cwl
(CommandLineTool)
|
||
| generate_cna_data |
copy_number.cwl
(CommandLineTool)
|
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| concat_hisens_segs |
concat.cwl
(Workflow)
|
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| 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)
|
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| concat_cbio_muts_maf |
concat-tables.cwl
(CommandLineTool)
|
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| convert_fusion_to_sv |
fusion_to_sv.cwl
(CommandLineTool)
|
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| generate_cases_cnaseq |
generate_cBioPortal_file.cwl
(CommandLineTool)
|
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| generate_cbio_meta_sv |
generate_cBioPortal_file.cwl
(CommandLineTool)
|
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| generate_cbio_meta_cna |
generate_cBioPortal_file.cwl
(CommandLineTool)
|
||
| update_cases_sequenced |
updateCaseList.cwl
(CommandLineTool)
|
||
| generate_cbio_cases_all |
generate_cBioPortal_file.cwl
(CommandLineTool)
|
||
| merge_msi_data_clinical |
merge-tables.cwl
(CommandLineTool)
|
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| merge_tmb_data_clinical |
merge-tables.cwl
(CommandLineTool)
|
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| rename_cbio_hisens_segs |
cp.cwl
(CommandLineTool)
|
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| update_extra_sample_ids |
7e2f606a5a0994bba9f9ecf8cf35cd86
(ExpressionTool)
|
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| generate_cases_sequenced |
generate_cBioPortal_file.cwl
(CommandLineTool)
|
||
| generate_cbio_meta_study |
generate_cBioPortal_file.cwl
(CommandLineTool)
|
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| replace_illogical_values |
replace.cwl
(CommandLineTool)
|
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| generate_cbio_fusions_data |
concat.cwl
(Workflow)
|
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| generate_cbio_meta_fusions |
generate_cBioPortal_file.cwl
(CommandLineTool)
|
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| generate_meta_cna_segments |
generate_cBioPortal_file.cwl
(CommandLineTool)
|
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| reduce_sig_figs_hisens_segs |
reduce_sig_figs.cwl
(CommandLineTool)
|
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| generate_data_clinical_sample |
generate_cBioPortal_file.cwl
(CommandLineTool)
|
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| generate_meta_clinical_sample |
generate_cBioPortal_file.cwl
(CommandLineTool)
|
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| 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_meta_sv_file | File | ||
| portal_sv_data_file | 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 |
Permalink:
https://w3id.org/cwl/view/git/59b69eed7ffefcffd81313ec8ffb84c0d716b933/cwl/portal-workflow.cwl
