Workflow: Varscan Workflow
Fetched 2018-07-01 15:10:27 GMT
Verified with cwltool version 1.0.20180525185854
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
https://raw.githubusercontent.com/genome/arvados_trial/master/LICENSE
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| reference | File | ||
| normal_bam | File | ||
| tumor_bam | File | ||
| interval_list | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| bgzip_and_index_snvs |
bgzip_and_index.cwl
(Workflow)
|
bgzip and index VCF | |
| index_indels |
../detect_variants/index.cwl
(CommandLineTool)
|
vcf index | |
| varscan |
varscan.cwl
(Workflow)
|
varscan somatic workflow | |
| bgzip_and_index_indels |
bgzip_and_index.cwl
(Workflow)
|
bgzip and index VCF | |
| merge |
../detect_variants/merge.cwl
(CommandLineTool)
|
vcf merge | |
| bgzip_and_index_hc_indels |
bgzip_and_index.cwl
(Workflow)
|
bgzip and index VCF | |
| merge_snvs |
set_filter_status.cwl
(CommandLineTool)
|
create filtered VCF | |
| intervals_to_bed |
intervals_to_bed.cwl
(CommandLineTool)
|
||
| index |
../detect_variants/index.cwl
(CommandLineTool)
|
vcf index | |
| index_snvs |
../detect_variants/index.cwl
(CommandLineTool)
|
vcf index | |
| bgzip_and_index_hc_snvs |
bgzip_and_index.cwl
(Workflow)
|
bgzip and index VCF | |
| merge_indels |
set_filter_status.cwl
(CommandLineTool)
|
create filtered VCF |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| merged_vcf | File | ||
| indels | File | ||
| snvs | File |
Permalink:
https://w3id.org/cwl/view/git/4cded2c595b2ff83046729cd230f5ad34be3137d/varscan/workflow.cwl
