Workflow: Creates a FastJ file for each gVCF by path
Fetched 2023-01-14 11:43:02 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Requires:
This workflow is Open Source and may be reused according to the terms of:
GNU Affero General Public License v3.0
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| afn | File | Compressed assembly fixed width file | |
| ref | String | Reference genome | |
| afnM | File | Compressed mitochondrial assembly fixed width file | |
| aidx | File | Assembly index file | |
| refM | String | Mitochondrial reference genome | |
| aidxM | File | Mitochondrial assembly index file | |
| reffa | File | Reference genome in FASTA format | |
| reffaM | File | Reference mitochondrial genome in FASTA format | |
| seqidM | String | Mitochondrial naming scheme for gVCF | |
| tagdir | File | Compressed tagset in FASTA format | |
| refdirectory | Directory | Directory of input gVCFs |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| step1 |
getdirs.cwl
(ExpressionTool)
|
Create list of gVCF directories to process | |
| step2 |
convertgvcf.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| out1 | Directory[] | Directories of FastJs |
Permalink:
https://w3id.org/cwl/view/git/2d067e70af7c1a49a2a015ddcd0d859b0b885e98/cwl-version/convert2fastj/gvcf_version/cwl/tiling_convert2fastj_gvcf.cwl
