Workflow: main-vg.cwl
Fetched 2026-09-24 14:46:42 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:
BSD 3-clause "New" or "Revised" License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| ref | File | ||
| hapl | File | ||
| graph | File | ||
| reads1 | File | ||
| reads2 | File | ||
| regions | File (Optional) | ||
| model_type | String | ||
| output_vcf | File (Optional) | ||
| ref_prefix | String | ||
| output_cram | String (Optional) | ||
| output_gvcf | File (Optional) | ||
| dv_extra_args | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| kmc |
kmc.cwl
(CommandLineTool)
|
||
| vg-paths |
vg-paths.cwl
(CommandLineTool)
|
||
| vg-giraffe |
vg-giraffe.cwl
(CommandLineTool)
|
||
| deepvariant |
deepvariant.cwl
(CommandLineTool)
|
||
| samtools_sort |
samtools-sort.cwl
(CommandLineTool)
|
||
| samtools_index |
samtools-index.cwl
(CommandLineTool)
|
||
| samtools_stats |
samtools-stats.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| output_vcf | File (Optional) | ||
| output_gvcf | File (Optional) | ||
| aligned_reads | File | ||
| aligned_reads_stats | File |
Permalink:
https://w3id.org/cwl/view/git/0f513ee017a4b8c8aa1c2e6ca26b203a7d6f3800/workflows/variant-calling/main-vg.cwl
