Workflow: module-6
Fetched 2023-01-13 04:09:22 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| genome | String | ||
| vep_data | String | ||
| tumor_bam | File | ||
| delly_type | String[] | ||
| normal_bam | File | ||
| tumor_sample_name | String | ||
| normal_sample_name | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| index |
cmo-index/1.0.0/cmo-index.cwl
(CommandLineTool)
|
cmo-index | |
| createTNPair |
module-6.cwl#createTNPair/e0f9034a-490d-47b8-8ad8-1af5855e1945
(CommandLineTool)
|
||
| convert_vcf2maf |
cmo-vcf2maf/1.6.17/cmo-vcf2maf.cwl
(CommandLineTool)
|
cmo-vcf2maf |
None |
| call_sv_by_delly | |||
| merge_with_bcftools |
module-6.cwl#merge_with_bcftools/5671c969-9d82-4bdf-ab0c-46fbe8d90203
(CommandLineTool)
|
||
| portal_format_output |
portal-formatting.cli/1.0.0/format-maf.cwl
(Workflow)
|
format-maf | |
| merge_with_bcftools_unfiltered |
module-6.cwl#merge_with_bcftools_unfiltered/187c482b-b7c2-4f31-9e95-bfa08ab0e372
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| delly_sv | File[] | ||
| maf_file | File | ||
| merged_file | File | ||
| portal_file | File | ||
| delly_filtered_sv | File[] | ||
| merged_file_unfiltered | File |
Permalink:
https://w3id.org/cwl/view/git/49d7810b6446d6aadfcdbb6b5deee9f02ad749c2/setup/cwl/module-6.cwl
