Workflow: module-3.cwl
Fetched 2024-06-25 00:37:49 GMT
Verified with cwltool version 3.1.20230201224320
- 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 |
|---|---|---|---|
| dbsnp | File | ||
| cosmic | File | ||
| bed_file | File | ||
| ref_fasta | File | ||
| run_tools | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/variants_tools.yaml#run_tools | ||
| tumor_bams | File[] | ||
| normal_bams | File[] | ||
| mutect_params | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/params/mutect.yaml#mutect_params | ||
| vardict_params | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/params/vardict.yaml#vardict_params | ||
| bcftools_params | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/params/bcftools.yaml#bcftools_params | ||
| tumor_sample_names | String[] | ||
| normal_sample_names | String[] | ||
| annotate_concat_header_file | File | ||
| basicfiltering_mutect_params | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/params/basic-filtering-mutect.yaml#basicfiltering_mutect_params | ||
| basicfiltering_vardict_params | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/params/basic-filtering-vardict.yaml#basicfiltering_vardict_params |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| filtering |
subworkflows/filtering.cwl
(Workflow)
|
||
| concatenate |
subworkflows/vcf_concat.cwl
(Workflow)
|
||
| call_variants |
subworkflows/call_variants.cwl
(Workflow)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| mutect_vcf | File[] | ||
| vardict_vcf | File[] | ||
| concatenated_vcf | File[] | ||
| mutect_callstats | File[] | ||
| mutect_normalized_vcf | File[] | ||
| vardict_normalized_vcf | File[] | ||
| annotated_concatenated_vcf | File[] |
Permalink:
https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/workflows/module-3.cwl
