{"id":31063918,"url":"https://github.com/pmiddend/crystfel-cwl","last_synced_at":"2026-02-14T00:03:51.782Z","repository":{"id":310100696,"uuid":"1038538893","full_name":"pmiddend/crystfel-cwl","owner":"pmiddend","description":"Common Workflow Language (CWL) files for CrystFEL","archived":false,"fork":false,"pushed_at":"2025-08-15T11:45:56.000Z","size":6,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":0,"default_branch":"main","last_synced_at":"2025-10-11T19:42:31.236Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Common Workflow Language","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/pmiddend.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2025-08-15T11:45:34.000Z","updated_at":"2025-08-15T11:46:01.000Z","dependencies_parsed_at":"2025-08-16T14:47:31.895Z","dependency_job_id":null,"html_url":"https://github.com/pmiddend/crystfel-cwl","commit_stats":null,"previous_names":["pmiddend/crystfel-cwl"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/pmiddend/crystfel-cwl","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pmiddend%2Fcrystfel-cwl","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pmiddend%2Fcrystfel-cwl/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pmiddend%2Fcrystfel-cwl/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pmiddend%2Fcrystfel-cwl/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/pmiddend","download_url":"https://codeload.github.com/pmiddend/crystfel-cwl/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pmiddend%2Fcrystfel-cwl/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29424636,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-13T22:20:51.549Z","status":"ssl_error","status_checked_at":"2026-02-13T22:20:49.838Z","response_time":78,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2025-09-15T13:56:31.700Z","updated_at":"2026-02-14T00:03:51.764Z","avatar_url":"https://github.com/pmiddend.png","language":"Common Workflow Language","funding_links":[],"categories":[],"sub_categories":[],"readme":"# crystfel-cwl: Common Workflow Language (CWL) definitions for CrystFEL\n\nHere 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.\n\n## Benefits\n\n- 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.\n\n## How to run\n\nInstall [toil](http://toil.ucsc-cgl.org/) with CWL support (preferably in a virtual environment or similar):\n\n```\npip install toil[cwl]\n```\n\nThen run \"turbo indexer\" producing a single .stream file and a .geometry file as output:\n\n```\ntoil-cwl-runner turbo_index.cwl --geometry path/to/geometry.geom --masterfile path/to/master.h5 --cell path/to/cell-file --listprefix turbolist --linesperfile 1000\n```\n\nIf you want to run it on SLURM, for example, add *at least*: `--batchSystem slurm`. At DESY, the following additional options work best:\n\n```\n--jobStore my-job-store --slurmPartition allcpu --slurmTime 01-00:00:00 --slurmDefaultAllMem True --retryCount 2 --bypass-file-store\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpmiddend%2Fcrystfel-cwl","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpmiddend%2Fcrystfel-cwl","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpmiddend%2Fcrystfel-cwl/lists"}