https://github.com/midnighter/nextflow-gotchas

A collection of unexpected challenges and learnings with nextflow and nf-core.
https://github.com/midnighter/nextflow-gotchas

gotcha nextflow nextflow-pipeline nextflow-process nextflow-workflow nf-core

Last synced: 11 days ago
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A collection of unexpected challenges and learnings with nextflow and nf-core.

• Host: GitHub
• URL: https://github.com/midnighter/nextflow-gotchas
• Owner: Midnighter
• License: cc-by-sa-4.0
• Created: 2022-04-01T09:21:27.000Z (over 2 years ago)
• Default Branch: main
• Last Pushed: 2023-10-17T20:24:23.000Z (about 1 year ago)
• Last Synced: 2024-04-16T03:31:29.047Z (7 months ago)
• Topics: gotcha, nextflow, nextflow-pipeline, nextflow-process, nextflow-workflow, nf-core
• Language: Shell
• Homepage: https://midnighter.github.io/nextflow-gotchas/
• Size: 707 KB
• Stars: 34
• Watchers: 3
• Forks: 9
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# Nextflow Gotchas

[![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)

A 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.

## Usage

The 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:

-   [`docs/`](docs/) contains the markdown source files

-   [`examples/`](examples/) holds the nextflow workflows

At 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.

## Contributing

Contributions 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.

## Contributors ✨

Thanks go to these wonderful people ([emoji key](https://allcontributors.org/docs/en/emoji-key)):

  

    
FriederikeHanssen
📖 💡

    
James A. Fellows Yates
📖 💡

    
Simon Pearce
📖 💡

  

This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. Contributions of any kind welcome!

## Acknowledgements

As 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:

-   [Friederike Hanssen](https://github.com/FriederikeHanssen)

-   [Harshil Patel](https://github.com/drpatelh)

-   [Jose Espinosa-Carrasco](https://github.com/JoseEspinosa)

-   [Mahesh Binzer-Panchal](https://github.com/mahesh-panchal)

-   [Maxime U. Garcia](https://github.com/maxulysse)

-   [Phil Ewels](https://github.com/ewels)

-   [Pontus Freyhult](https://github.com/pontus)

-   [Robert Syme](https://github.com/robsyme)

If you feel that I forgot you in this list. Please let me know, it's not intentional!

## Copyright



All examples and descriptions are licensed under the Creative Commons Attribution-ShareAlike 4.0 International License.