Initial release of nf-core/rnaseq! 🎉
This release marks the point where the pipeline was moved from SciLifeLab/NGI-RNAseq
over to the new nf-core community, at nf-core/rnaseq.
You can view the previous changelog at SciLifeLab/NGI-RNAseq/CHANGELOG.md
In addition to porting to the new nf-core community, the pipeline has had a number of major changes in this version. There have been 157 commits by 16 different contributors covering 70 different files in the pipeline: 7,357 additions and 8,236 deletions!
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
- Support for GFF files in addition to GTF files
- Just use
--gffinstead of--gtfwhen specifying a file path
- Just use
- New command line options to skip various quality control steps
- More safety checks when launching a pipeline
- Several new sanity checks - for example, that the specified reference genome exists
- Improved performance with memory usage (especially STAR and Picard)
- New BigWig file outputs for plotting coverage across the genome
- Refactored gene body coverage calculation, now much faster and using much less memory
- Bugfixes in the MultiQC process to avoid edge cases where it wouldn't run
- MultiQC report now automatically attached to the email sent when the pipeline completes
- New testing method, with data on GitHub
- Now run pipeline with
-profile testinstead of using bash scripts
- Now run pipeline with
- Rewritten continuous integration tests with Travis CI
- New explicit support for Singularity containers
- Improved MultiQC support for DupRadar and featureCounts
- Now works for all users instead of just NGI Stockholm
- New configuration for use on AWS batch
- Updated config syntax to support latest versions of Nextflow
- Built-in support for a number of new local HPC systems
- CCGA, GIS, UCT HEX, updates to UPPMAX, CFC, BINAC, Hebbe, c3se
- Slightly improved documentation (more updates to come)
- Updated software packages
...and many more minor tweaks.
Thanks to everyone who has worked on this release!