Workflow: Varscan Workflow
Fetched 2023-01-13 08:06:43 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 |
|---|---|---|---|
| p_value | Float (Optional) | ||
| reference | String | ||
| tumor_bam | File | ||
| normal_bam | File | ||
| min_coverage | Integer (Optional) | ||
| min_var_freq | Float (Optional) | ||
| interval_list | File | ||
| strand_filter | Integer (Optional) | ||
| max_normal_freq | Float (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| index |
../tools/index_vcf.cwl
(CommandLineTool)
|
vcf index | |
| merge |
../tools/merge_vcf.cwl
(CommandLineTool)
|
vcf merge | |
| filter |
fp_filter.cwl
(Workflow)
|
fp_filter workflow | |
| varscan |
varscan.cwl
(Workflow)
|
varscan somatic workflow | |
| index_snvs |
../tools/index_vcf.cwl
(CommandLineTool)
|
vcf index | |
| merge_snvs |
../tools/set_filter_status.cwl
(CommandLineTool)
|
create filtered VCF | |
| index_indels |
../tools/index_vcf.cwl
(CommandLineTool)
|
vcf index | |
| merge_indels |
../tools/set_filter_status.cwl
(CommandLineTool)
|
create filtered VCF | |
| intervals_to_bed |
../tools/intervals_to_bed.cwl
(CommandLineTool)
|
||
| bgzip_and_index_snvs |
bgzip_and_index.cwl
(Workflow)
|
bgzip and index VCF | |
| bgzip_and_index_indels |
bgzip_and_index.cwl
(Workflow)
|
bgzip and index VCF | |
| bgzip_and_index_hc_snvs |
bgzip_and_index.cwl
(Workflow)
|
bgzip and index VCF | |
| bgzip_and_index_hc_indels |
bgzip_and_index.cwl
(Workflow)
|
bgzip and index VCF |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| filtered_vcf | File | ||
| unfiltered_vcf | File |
Permalink:
https://w3id.org/cwl/view/git/f9600f9959acdc30259ba7e64de61104c9b01f0b/definitions/subworkflows/varscan_pre_and_post_processing.cwl
