Workflow: module-6
Fetched 2023-01-12 17:41:03 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/a758395d-522c-4092-becd-8f05d2316d6e
(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/777a1173-6415-41d5-9d1c-e60bcfb105f8
(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/b8bbf38e-91bf-440d-a063-f8c7c16a88ea
(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/5b6fb984f3cf8e971d677c92a096cd437f34b787/setup/cwl/module-6.cwl
