Workflow: Convert FastJs to npy arrays for gVCF input
Fetched 2023-01-10 07:34:57 GMT
Verified with cwltool version 3.1.20221201130942
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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 | |
| fjdir | Directory | Directory of FastJ files | |
| reffa | File | Reference genome in FASTA format | |
| chroms | String[] | Chromosomes to analyze | |
| srclib | Directory (Optional) | Existing tile library directory | |
| tagset | File | Compressed tagset in FASTA format | |
| gvcfdir | Directory | Input gVCF directory | |
| nchunks | String | Number of chunks to scatter | |
| pathmax | String | Last/Maximum path in the tile library | |
| pathmin | String | Starting path in the tile library | |
| checknum | Integer | Number of samples to check | |
| checkchroms | String[] | Chromosomes to validate | |
| sglfthreshold | Integer | Threshold for unzipped sglf size in MiB |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| createnpy-wf |
../npy/createnpy-wf.cwl
(Workflow)
|
Create NumPy arrays by tile path from cgfs, merge all NumPy arrays into single array | |
| fastj2cgf-wf |
fastj2cgf-wf.cwl
(Workflow)
|
Convert FastJs to cgfs | |
| check-cgf-gvcf-wf | Workflow to validate the the gVCF to cgf conversion |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| lib | Directory | Tile library directory | |
| names | File | File listing sample names | |
| cgfdir | Directory | Output cgfs | |
| sglfsize | File | Unzipped sglf size | |
| skippaths | File | Paths to skip | |
| consolnpydir | Directory | Output consolidated NumPy arrays |
Permalink:
https://w3id.org/cwl/view/git/cdfe9178ad4e481d2391cd2da74b82d66a61b0bb/cwl-version/masterworkflow/fastj2npy-wf.cwl
