Workflow: samples_fillout_workflow.cwl
Fetched 2023-01-03 21:50:52 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 |
|---|---|---|---|
| bam_files | File[] | ||
| maf_files | File[] | ||
| ref_fasta | File | ||
| sample_ids | String[] | ||
| exac_filter | File | ||
| output_fname | String (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| gbcms |
samples_fillout_workflow.cwl#gbcms/f1d8d8ab-b7a6-4268-9705-6c785c86da08
(CommandLineTool)
|
||
| maf2vcf |
samples_fillout_workflow.cwl#maf2vcf/b562d5e9-5ff0-4496-8735-78d3678faed5
(CommandLineTool)
|
||
| merge_vcfs |
samples_fillout_workflow.cwl#merge_vcfs/b15d171e-82f3-40c2-8b6d-7e3659529504
(CommandLineTool)
|
||
| split_vcf_to_mafs |
samples_fillout_workflow.cwl#split_vcf_to_mafs/502783cf-63b8-42ec-b9cf-95d877a82667
(CommandLineTool)
|
||
| concat_with_comments |
samples_fillout_workflow.cwl#concat_with_comments/dfe0ca68-13a2-497a-a324-4ab675ba79ef
(CommandLineTool)
|
||
| fix_labels_and_merge_vcfs |
samples_fillout_workflow.cwl#fix_labels_and_merge_vcfs/3829df36-9f0d-4fb5-aedb-173e9191d604
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| output_file | File |
Permalink:
https://w3id.org/cwl/view/git/7eb2b0a4d37018142233d770595ac2e00376dab4/cwl/samples_fillout_workflow.cwl
