{"id":19221045,"url":"https://github.com/midnighter/nextflow-gotchas","last_synced_at":"2025-05-13T01:14:59.791Z","repository":{"id":38314940,"uuid":"476654227","full_name":"Midnighter/nextflow-gotchas","owner":"Midnighter","description":"A collection of unexpected challenges and learnings with nextflow and nf-core.","archived":false,"fork":false,"pushed_at":"2023-10-17T20:24:23.000Z","size":724,"stargazers_count":37,"open_issues_count":2,"forks_count":9,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-05-13T01:14:52.623Z","etag":null,"topics":["gotcha","nextflow","nextflow-pipeline","nextflow-process","nextflow-workflow","nf-core"],"latest_commit_sha":null,"homepage":"https://midnighter.github.io/nextflow-gotchas/","language":"Shell","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"cc-by-sa-4.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Midnighter.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","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}},"created_at":"2022-04-01T09:21:27.000Z","updated_at":"2025-04-22T09:49:46.000Z","dependencies_parsed_at":"2024-11-09T14:42:44.451Z","dependency_job_id":"caa4c59a-8d55-4e81-b1a0-8cf64962ef15","html_url":"https://github.com/Midnighter/nextflow-gotchas","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Midnighter%2Fnextflow-gotchas","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Midnighter%2Fnextflow-gotchas/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Midnighter%2Fnextflow-gotchas/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Midnighter%2Fnextflow-gotchas/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Midnighter","download_url":"https://codeload.github.com/Midnighter/nextflow-gotchas/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":253851074,"owners_count":21973674,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","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":["gotcha","nextflow","nextflow-pipeline","nextflow-process","nextflow-workflow","nf-core"],"created_at":"2024-11-09T14:39:46.841Z","updated_at":"2025-05-13T01:14:59.765Z","avatar_url":"https://github.com/Midnighter.png","language":"Shell","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Nextflow Gotchas\n\n[![Gitpod Ready-to-Code](https://img.shields.io/badge/Gitpod-Ready--to--Code-blue?logo=gitpod)](https://gitpod.io/#https://github.com/Midnighter/nextflow-gotchas)\n\nA collection of unexpected challenges and learnings with [nextflow](https://nextflow.io/) and [nf-core](https://nf-co.re/). The provided examples reflect my journey in learning nextflow and generally assume an intermediate familiarity with nextflow.\n\n## Usage\n\nThe contents of this repository are best enjoyed from [the rendered site](https://midnighter.github.io/nextflow-gotchas). The site is generated using [mkdocs-material](https://squidfunk.github.io/mkdocs-material/) and organized as follows:\n\n-   [`docs/`](docs/) contains the markdown source files\n-   [`examples/`](examples/) holds the nextflow workflows\n\nAt any point, you can also explore the documentation and examples interactively. Either by [opening the project in a Gitpod]() which comes pre-installed with the dependencies to serve the documentation, as well as nextflow to run the examples. Or by cloning the repository and exploring it with your favorite editor and run nextflow locally.\n\n## Contributing\n\nContributions are most welcome and I very much aim for this to be a community-driven project. In fact, most of the solutions provided here came from discussions on the [nextflow](https://join.slack.com/t/nextflow/shared_invite/zt-11iwlxtw5-R6SNBpVksOJAx5sPOXNrZg) or [nf-core Slack](https://nfcore.slack.com/). Both are incredible communities and I can only recommend that you join. Please [open an issue on the repository](https://github.com/Midnighter/nextflow-gotchas/issues) if you have a good example, an idea, or any other suggestion.\n\n## Contributors ✨\n\nThanks go to these wonderful people ([emoji key](https://allcontributors.org/docs/en/emoji-key)):\n\n\u003c!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section --\u003e\n\u003c!-- prettier-ignore-start --\u003e\n\u003c!-- markdownlint-disable --\u003e\n\u003ctable\u003e\n  \u003ctr\u003e\n    \u003ctd align=\"center\"\u003e\u003ca href=\"https://github.com/FriederikeHanssen\"\u003e\u003cimg src=\"https://avatars.githubusercontent.com/u/12273093?v=4?s=110\" width=\"110px;\" alt=\"\"/\u003e\u003cbr /\u003e\u003csub\u003e\u003cb\u003eFriederikeHanssen\u003c/b\u003e\u003c/sub\u003e\u003c/a\u003e\u003cbr /\u003e\u003ca href=\"https://github.com/Midnighter/nextflow-gotchas/commits?author=FriederikeHanssen\" title=\"Documentation\"\u003e📖\u003c/a\u003e \u003ca href=\"#example-FriederikeHanssen\" title=\"Examples\"\u003e💡\u003c/a\u003e\u003c/td\u003e\n    \u003ctd align=\"center\"\u003e\u003ca href=\"https://github.com/jfy133\"\u003e\u003cimg src=\"https://avatars.githubusercontent.com/u/17950287?v=4?s=110\" width=\"110px;\" alt=\"\"/\u003e\u003cbr /\u003e\u003csub\u003e\u003cb\u003eJames A. Fellows Yates\u003c/b\u003e\u003c/sub\u003e\u003c/a\u003e\u003cbr /\u003e\u003ca href=\"https://github.com/Midnighter/nextflow-gotchas/commits?author=jfy133\" title=\"Documentation\"\u003e📖\u003c/a\u003e \u003ca href=\"#example-jfy133\" title=\"Examples\"\u003e💡\u003c/a\u003e\u003c/td\u003e\n    \u003ctd align=\"center\"\u003e\u003ca href=\"https://github.com/SPPearce\"\u003e\u003cimg src=\"https://avatars.githubusercontent.com/u/24893913?v=4?s=110\" width=\"110px;\" alt=\"\"/\u003e\u003cbr /\u003e\u003csub\u003e\u003cb\u003eSimon Pearce\u003c/b\u003e\u003c/sub\u003e\u003c/a\u003e\u003cbr /\u003e\u003ca href=\"https://github.com/Midnighter/nextflow-gotchas/commits?author=SPPearce\" title=\"Documentation\"\u003e📖\u003c/a\u003e \u003ca href=\"#example-SPPearce\" title=\"Examples\"\u003e💡\u003c/a\u003e\u003c/td\u003e\n  \u003c/tr\u003e\n\u003c/table\u003e\n\n\u003c!-- markdownlint-restore --\u003e\n\u003c!-- prettier-ignore-end --\u003e\n\n\u003c!-- ALL-CONTRIBUTORS-LIST:END --\u003e\n\nThis project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. Contributions of any kind welcome!\n\n## Acknowledgements\n\nAs mentioned, nextflow has an amazing community. I want to mention a few people here who have been especially helpful in my interactions. In alphabetical order:\n\n-   [Friederike Hanssen](https://github.com/FriederikeHanssen)\n-   [Harshil Patel](https://github.com/drpatelh)\n-   [Jose Espinosa-Carrasco](https://github.com/JoseEspinosa)\n-   [Mahesh Binzer-Panchal](https://github.com/mahesh-panchal)\n-   [Maxime U. Garcia](https://github.com/maxulysse)\n-   [Phil Ewels](https://github.com/ewels)\n-   [Pontus Freyhult](https://github.com/pontus)\n-   [Robert Syme](https://github.com/robsyme)\n\nIf you feel that I forgot you in this list. Please let me know, it's not intentional!\n\n## Copyright\n\n\u003ca rel=\"license\" href=\"http://creativecommons.org/licenses/by-sa/4.0/\"\u003e\u003cimg alt=\"Creative Commons License\" style=\"border-width:0\" src=\"https://i.creativecommons.org/l/by-sa/4.0/88x31.png\" /\u003e\u003c/a\u003e\n\nAll examples and descriptions are licensed under the \u003ca rel=\"license\" href=\"http://creativecommons.org/licenses/by-sa/4.0/\"\u003eCreative Commons Attribution-ShareAlike 4.0 International License\u003c/a\u003e.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmidnighter%2Fnextflow-gotchas","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmidnighter%2Fnextflow-gotchas","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmidnighter%2Fnextflow-gotchas/lists"}