Please consider using/contributing to https://github.com/nf-core/sarek
Initial release of nf-core/deepvariant! 🎉
This release marks the point where the pipeline was moved from lifebit-ai/DeepVariant over to the new nf-core community, at nf-core/DeepVariant. The nf-core template was used to help ensure that the pipeline meets the standards of nf-core.
In summary, the main changes are:
- Rebranding and renaming throughout the pipeline to nf-core
- Updating many parts of the pipeline config and style to meet nf-core standards
- Continuous integration tests with Travis CI
- Dependencies installed via conda
- Added support for BAM input as file, not just a folder
- Added channels to process input files
- Added separate processes for each of the steps in FASTA file preprocessing
- Use of genomes config to specify relevant reference genome files similar to igenomes
- Added BAM size dependent setting of memory
- Slightly improved documentation
…and many more minor tweaks.
Thanks to everyone who has worked on this release!