CI
6f2f840fd9
Build pipeline: viash-hub.biobox.main-zp6tq
Source commit: 7f8bcc2b3e
Source message: BD rhapsody sequence analysis (#96)
* wip
* fix test
* add help
* update 2.2 args
* fix bug
* extend test data
* output separate files
* analyse missing args
* tweaks to test
* fix script
* fix test
* fix test
* move small reference
* wip generate wta test data
* don't forget about umi in r1
* remove unneeded pkg
* load reference in memory just once
* fix random choices
* extend test
* add abc immunediscoverypanel
* wip abc testing code
* fix abc test; need unique instrument, run and flowcell ids for each sample
* add smk data
* add entry to changelog
* remove old test file
* adapt test for missing read
* update description
* add comment
* ensure cwl files are absolute
* Apply suggestions from code review
Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>
* fix suggestion
* newer pipelines have docker requirements as a hint instead of a strict requirement
* rename str to content
* remove deleted resources
* fix containers
* fix script
* fix suggestion
* fix suggestion...
* fix test
* fix component name
* fix test
* apply suggestions
* fix test
* added note
* fix changelog
* fix changelog again
* splitting hairs here
---------
Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>
🌱📦 biobox
A collection of bioinformatics tools for working with sequence data.
Objectives
- Reusability: Facilitating the use of components across various projects and contexts.
- Reproducibility: Ensuring that components are reproducible and can be easily shared.
- Best Practices: Adhering to established standards in software development and bioinformatics.
Contributing
We encourage contributions from the community. To contribute:
- Fork the Repository: Start by forking this repository to your account.
- Develop Your Component: Create your Viash component, ensuring it aligns with our best practices (detailed below).
- Submit a Pull Request: After testing your component, submit a pull request for review.
Contribution Guidelines
The contribution guidelines describes which steps you should follow to contribute a component to this repository.
- Find a component to contribute
- Add config template
- Fill in the metadata
- Find a suitable container
- Create help file
- Create or fetch test data
- Add arguments for the input files
- Add arguments for the output files
- Add arguments for the other arguments
- Add a Docker engine
- Write a runner script
- Create test script
- Create a
/var/software_versions.txtfile
See the CONTRIBUTING file for more details.
Support and Community
For support, questions, or to join our community:
- Issues: Submit questions or issues via the GitHub issue tracker.
- Discussions: Join our discussions via GitHub Discussions.
License
This repository is licensed under an MIT license. See the LICENSE file for details.