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@ewels ewels released this 20 Aug 16:39
· 4707 commits to master since this release
1.0
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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 --gff instead of --gtf when specifying a file path
  • 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 test instead of using bash scripts
  • 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!

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