Workflow: Convert FastJs to cgfs
Fetched 2023-01-10 07:06:24 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
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 |
|---|---|---|---|
| fjdir | Directory | Directory of FastJ files | |
| srclib | Directory (Optional) | Existing tile library directory | |
| tagset | File | Compressed tagset in FASTA format | |
| nchunks | String | Number of chunks to scatter | |
| pathmax | String | Last/Maximum path in the tile library | |
| pathmin | String | Starting path in the tile library | |
| sglfthreshold | Integer | Threshold for unzipped sglf size in MiB |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| getsglfsize |
../checks/check-sglf/getsglfsize.cwl
(CommandLineTool)
|
Get unzipped sglf size and find paths above a given threshold | |
| handle-cgfs |
expressiontool/array-to-dir.cwl
(ExpressionTool)
|
||
| createcgf-wf |
../cgf3/createcgf-wf.cwl
(Workflow)
|
Creates a cgf for each FastJ file | |
| handle-sglfs |
expressiontool/nestedarray-to-dir.cwl
(ExpressionTool)
|
||
| createsglf-wf |
../tilelib/createsglf-wf.cwl
(Workflow)
|
Create a tile library (SGLF) for a given set of FastJ files | |
| merge-tilelib |
../tilelib/merge-tilelib.cwl
(CommandLineTool)
|
Merges new tile library into existing tile library | |
| sglf-sanity-check |
../checks/check-sglf/sglf-sanity-check.cwl
(CommandLineTool)
|
Check tile library for correct formatting and spurious characters |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| lib | Directory | Tile library directory | |
| cgfdir | Directory | Output cgfs | |
| sglfsize | File | Unzipped sglf size | |
| skippaths | File | Paths to skip |
Permalink:
https://w3id.org/cwl/view/git/cdfe9178ad4e481d2391cd2da74b82d66a61b0bb/cwl-version/masterworkflow/fastj2cgf-wf.cwl
