Workflow: vcf_concat.cwl
Fetched 2024-05-19 15:36:05 GMT
Verified with cwltool version 3.1.20230201224320
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- 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 |
|---|---|---|---|
| run_tools | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/variants_tools.yaml#run_tools | ||
| vcf_mutect | File | ||
| vcf_vardict | File | ||
| bcftools_params | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/params/bcftools.yaml#bcftools_params | ||
| tumor_sample_name | String | ||
| normal_sample_name | String | ||
| annotate_concat_input_header | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| concat |
../../cwl_tools/bcftools/bcftools_concat.cwl
(CommandLineTool)
|
concatenate VCF/BCF files from the same set of samples |
|
| annotate_concat |
../../cwl_tools/concatVCF/annotate_concat.cwl
(CommandLineTool)
|
Annotates common variants in concatenated vcf and another vcf with tag from inputted header file |
|
| create_vcf_file_array |
vcf_concat.cwl#create_vcf_file_array/6f003ef4-8625-49d6-a6fe-e5160f0720a5
(ExpressionTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| combined_vcf | File | ||
| annotated_combined_vcf | File |
Permalink:
https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/workflows/subworkflows/vcf_concat.cwl
