Workflow: samples_fillout_workflow.cwl
Fetched 2026-02-04 15:04:53 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/c10d8bcf045067b3510bff68e2e957fccea0d7ea/cwl/types.yml#FilloutSample[] | ||
| ref_fasta | File | ||
| exac_filter | File | ||
| output_fname | String (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| gbcms |
56f43f66820bb60df10c56dccb2e4f43
(CommandLineTool)
|
||
| maf2vcf |
256c9e1605c904c2ff44474a4d47f337
(CommandLineTool)
|
||
| merge_vcfs |
aad62a774c3e24c35deb15bdd9707e5e
(CommandLineTool)
|
||
| vcf_to_maf |
55f931d29afaf6af270d8683f69f7561
(CommandLineTool)
|
||
| create_bam_list |
b762de9d3790b600bfe3a52792160616
(ExpressionTool)
|
||
| make_filter_args |
2c3aa4ea73f43bdb7d30b4b8c18030cf
(ExpressionTool)
|
||
| split_filter_vcf |
c46c298a4bfc665f0d061b6f1186f5e1
(CommandLineTool)
|
||
| create_samples_list |
f105f5973028d9d3a3c5c121b91b9c40
(ExpressionTool)
|
||
| concat_with_comments |
6a1d46947106e58efca7a07936f4b5da
(CommandLineTool)
|
||
| fix_labels_and_merge_vcfs |
f460908be597b36f079a86834769e950
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| output_file | File | ||
| filtered_file | File |
Permalink:
https://w3id.org/cwl/view/git/c10d8bcf045067b3510bff68e2e957fccea0d7ea/cwl/samples_fillout_workflow.cwl
