Workflow: samples_fillout_workflow.cwl
Fetched 2026-09-08 23:53:12 GMT
Verified with cwltool version 3.1.20230201224320
Workflow to run GetBaseCountsMultiSample fillout on a number of samples, each with their own bam and maf files
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| samples | https://w3id.org/cwl/view/git/45604eaeea15030c7302941c761464ce392abf74/cwl/types.yml#FilloutSample[] | ||
| ref_fasta | File | ||
| exac_filter | File | ||
| output_fname | String (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| gbcms |
5343a9dad6afac72693e477d1100ad7a
(CommandLineTool)
|
||
| maf2vcf |
abd4bba82fddb439fbe501f6574970d6
(CommandLineTool)
|
||
| vcf_to_maf |
1de362bc3fa667c5f45d547225baaef5
(CommandLineTool)
|
||
| create_bam_list |
7afdfdb790c91bada61b77f6b1ce4f72
(ExpressionTool)
|
||
| split_filter_vcf |
ec416fa0fdc651de0738446165c1cd3e
(CommandLineTool)
|
||
| create_samples_list |
bb2c72518bf8ec096921a261ba964ba0
(ExpressionTool)
|
||
| concat_with_comments |
f7b1be7c7bacd9d4b9357397e64de662
(CommandLineTool)
|
||
| convert_to_portal_format |
update_cBioPortal_data.cwl
(CommandLineTool)
|
||
| fix_labels_and_merge_vcfs |
7f2d31ca0e4891106ef953f0334b64e5
(CommandLineTool)
|
||
| create_fillout_targets_list |
c1eb3106576b32f6b389ac6c33a0a9fa
(CommandLineTool)
|
||
| create_clinical_samples_list |
08b475c43234a819b3cbe5f940bb532a
(ExpressionTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| output_file | File | ||
| portal_file | File | ||
| filtered_file | File |
Permalink:
https://w3id.org/cwl/view/git/45604eaeea15030c7302941c761464ce392abf74/cwl/samples_fillout_workflow.cwl
