Workflow: cnv_manta
Fetched 2024-10-23 02:55:08 GMT
Verified with cwltool version 3.1.20230201224320
CNV Manta 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 |
|---|---|---|---|
| bed | File |
bgzip-compressed/tabix-indexed BED file containing the set of regions to call |
|
| bams | File[] |
multiple BAM files representing a different sample |
|
| exome | Boolean |
set options for WES input: turn off depth filters |
|
| min_q | String | ||
| max_len | String | ||
| min_len | String | ||
| samples | File | ||
| reference_genome | File |
samtools-indexed reference FASTA file |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| manta_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_manta.cwl
