Version history

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!