Workflow: samples_fillout_workflow.cwl
Fetched 2026-08-08 05:30:36 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/5cad957fec135aa55ca8d588372db0557ca1cad5/cwl/types.yml#FilloutSample[] | ||
| ref_fasta | File | ||
| exac_filter | File | ||
| output_fname | String (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| gbcms |
32dbc91493843e40bc608a568c1f6b47
(CommandLineTool)
|
||
| maf2vcf |
1817c771944fccc9fd0bed381a2819ce
(CommandLineTool)
|
||
| vcf_to_maf |
c8d7c06ebcda0cd249ffbccdc3feaa29
(CommandLineTool)
|
||
| create_bam_list |
05ee7ea964630c8496ddb6bd79e8e112
(ExpressionTool)
|
||
| split_filter_vcf |
233f291e61ecaa7614145b3e36eafa5c
(CommandLineTool)
|
||
| create_samples_list |
e9f814edf821f65d1b826de8f5f320c1
(ExpressionTool)
|
||
| concat_with_comments |
1273b46214c943414be7c1549d9fd215
(CommandLineTool)
|
||
| convert_to_portal_format |
update_cBioPortal_data.cwl
(CommandLineTool)
|
||
| fix_labels_and_merge_vcfs |
e0786a21d8869bc974394c4b9e39b1a7
(CommandLineTool)
|
||
| create_fillout_targets_list |
dee6620e1cfd6925c929739f0eee36c1
(CommandLineTool)
|
||
| create_clinical_samples_list |
6a0f9fecae8ed3edb5856f19fd33b561
(ExpressionTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| output_file | File | ||
| portal_file | File | ||
| filtered_file | File |
Permalink:
https://w3id.org/cwl/view/git/5cad957fec135aa55ca8d588372db0557ca1cad5/cwl/samples_fillout_workflow.cwl
