Workflow: module-4.cwl
Fetched 2024-05-07 21:42:17 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
MIT License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| hotspots | File | ||
| ref_fasta | File | ||
| run_tools | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/variants_tools.yaml#run_tools | ||
| combine_vcf | File | ||
| exac_filter | File | ||
| gbcms_params | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/params/gbcms_params.yaml#gbcms_params | ||
| blacklist_file | File | ||
| vcf2maf_params | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/params/vcf2maf.yaml#vcf2maf_params | ||
| genotyping_bams | File[] | ||
| custom_enst_file | File | ||
| tumor_sample_name | String | ||
| normal_sample_name | String | ||
| genotyping_bams_ids | String[] | ||
| access_filters_params | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/params/access_filters.yaml#access_filters__params | ||
| matched_normal_sample_name | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| fillout |
../cwl_tools/gbcms/gbcms.cwl
(CommandLineTool)
|
||
| vcf2maf |
../cwl_tools/vcf2maf/vcf2maf.cwl
(CommandLineTool)
|
||
| tag_hotspots |
../cwl_tools/hotspots/tag_hotspots.cwl
(CommandLineTool)
|
||
| access_filters |
../cwl_tools/python/ACCESS_filters.cwl
(CommandLineTool)
|
||
| remove_variants_by_annotation |
../cwl_tools/remove_variants_by_anno/remove_variants_by_annotation.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| maf | File | ||
| fillout_maf | File | ||
| final_filtered_maf | File | ||
| kept_rmvbyanno_maf | File | ||
| dropped_rmvbyanno_maf | File | ||
| hotspots_filtered_maf | File | ||
| dropped_NGR_rmvbyanno_maf | File | ||
| final_filtered_condensed_maf | File |
Permalink:
https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/workflows/module-4.cwl
