Workflow: cnv_gridss
Fetched 2023-02-17 21:28:40 GMT
Verified with cwltool version 3.1.20230201224320
CNV GRIDSS calling
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
Apache License 2.0
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| bams | File[] |
multiple BAM files representing a different sample |
|
| min_q | String | ||
| max_len | String | ||
| min_len | String | ||
| samples | File | ||
| threads | Integer (Optional) |
number of threads to use. Defaults to 8 cores |
|
| blacklist | File (Optional) |
BED file containing regions to ignore (optional) |
|
| reference_genome | File |
reference genome to use. Must have a .fai index file and a bwa index |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| gridss_merge |
../tools/merge.cwl
(CommandLineTool)
|
merge |
Merge BED file |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| output | File |
Permalink:
https://w3id.org/cwl/view/git/70eec658fd1b92c4d0e3b24146820010b5983d41/structuralvariants/subworkflows/cnv_gridss.cwl
