Workflow: samples_fillout_workflow.cwl
Fetched 2023-01-08 23:50:31 GMT
Verified with cwltool version 3.1.20221201130942
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/ba3ff09328cc646d7254b2d2ee0fbe1abca3d4ad/cwl/types.yml#FilloutSample[] | ||
| ref_fasta | File | ||
| exac_filter | File | ||
| output_fname | String (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| gbcms |
cad0b72f0a5942d8a506065b66a05783
(CommandLineTool)
|
||
| maf2vcf |
e4105be2c5d2781524c190e9f453b5c3
(CommandLineTool)
|
||
| merge_vcfs |
9467b99c3d8f7c8690de26ed7c8ae2d5
(CommandLineTool)
|
||
| vcf_to_maf |
33fd5561eed5bcaba49ffa86916c488d
(CommandLineTool)
|
||
| create_bam_list |
a95da30b2d340fc605c59e6de863b7dc
(ExpressionTool)
|
||
| make_filter_args |
765d54999104dc3a7a88730ca735bd78
(ExpressionTool)
|
||
| split_filter_vcf |
34320e8dc3e54c73971cc99b76583994
(CommandLineTool)
|
||
| create_samples_list |
620f2247e3b4da24f8322643ce7b8f60
(ExpressionTool)
|
||
| concat_with_comments |
288b3150b15b6a65fdf88a89e3069afc
(CommandLineTool)
|
||
| fix_labels_and_merge_vcfs |
119de7e54f94262bb5e6243538de189e
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| output_file | File |
Permalink:
https://w3id.org/cwl/view/git/ba3ff09328cc646d7254b2d2ee0fbe1abca3d4ad/cwl/samples_fillout_workflow.cwl
