https://github.com/pmiddend/crystfel-cwl
Common Workflow Language (CWL) files for CrystFEL
https://github.com/pmiddend/crystfel-cwl
Last synced: 4 months ago
JSON representation
Common Workflow Language (CWL) files for CrystFEL
- Host: GitHub
- URL: https://github.com/pmiddend/crystfel-cwl
- Owner: pmiddend
- Created: 2025-08-15T11:45:34.000Z (10 months ago)
- Default Branch: main
- Last Pushed: 2025-08-15T11:45:56.000Z (10 months ago)
- Last Synced: 2025-10-11T19:42:31.236Z (8 months ago)
- Language: Common Workflow Language
- Size: 5.86 KB
- Stars: 0
- Watchers: 0
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# crystfel-cwl: Common Workflow Language (CWL) definitions for CrystFEL
Here you will find `.cwl` files, which represent [Common Workflow Language](https://www.commonwl.org/user_guide/index.html) definitions for DESY's [CrystFEL](https://www.desy.de/~twhite/crystfel/) serial crystallogaphy analysis suite.
## Benefits
- Support for multiple batch systems with the same CWL script. If you're using the [toil](http://toil.ucsc-cgl.org/) pipeline management system, you can run the scripts included in this repository using Slurm, HTCondor, Arvados, LSF, and many others, while still retaining performance.
## How to run
Install [toil](http://toil.ucsc-cgl.org/) with CWL support (preferably in a virtual environment or similar):
```
pip install toil[cwl]
```
Then run "turbo indexer" producing a single .stream file and a .geometry file as output:
```
toil-cwl-runner turbo_index.cwl --geometry path/to/geometry.geom --masterfile path/to/master.h5 --cell path/to/cell-file --listprefix turbolist --linesperfile 1000
```
If you want to run it on SLURM, for example, add *at least*: `--batchSystem slurm`. At DESY, the following additional options work best:
```
--jobStore my-job-store --slurmPartition allcpu --slurmTime 01-00:00:00 --slurmDefaultAllMem True --retryCount 2 --bypass-file-store
```