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nf-core/rnaseq: Changelog

Version 1.3

Pipeline Updates

  • Added configurable options to specify group attributes for featureCounts #144
  • Added support for RSeqC 3.0 #148
  • Added a parameters.settings.json file for use with the new nf-core launch helper tool.
  • Centralized all configuration profiles using nf-core/configs
  • Fixed all centralized configs for offline usage
  • Hide %dup in multiqc report

Bug fixes

  • Fixing HISAT2 Index Building for large reference genomes #153
  • Fixing HISAT2 BAM sorting using more memory than available on the system
  • Fixing MarkDuplicates memory consumption issues following #179

Dependency Updates

  • RSeQC 2.6.4 -> 3.0.0
  • Picard 2.18.15 -> 2.18.23
  • r-data.table 1.11.4 -> 1.12.0
  • r-markdown 0.8 -> 0.9
  • csvtk 0.15.0 -> 0.17.0
  • stringtie 1.3.4 -> 1.3.5
  • subread 1.6.2 -> 1.6.4
  • gffread 0.9.9 -> 0.9.12
  • multiqc 1.6 -> 1.7

Version 1.2 - 2018-12-12

Pipeline updates

  • Removed some outdated documentation about non-existent features
  • Config refactoring and code cleaning
  • Added a --fcExtraAttributes option to specify more than ENSEMBL gene names in featureCounts
  • Remove legacy rseqc strandRule config code. #119
  • Added STRINGTIE ballgown output to results folder #125
  • HiSAT index build now requests 200GB memory, enough to use the exons / splice junction option for building.
    • Added documentation about the --hisatBuildMemory option.
  • BAM indices are stored and re-used between processes #71

Bug Fixes

  • Fixed conda bug which caused problems with environment resolution due to changes in bioconda #113
  • Fixed wrong gffread command line #117
  • Added cpus = 1 to workflow summary process #130

Version 1.1 - 2018-10-05

Pipeline updates

  • Wrote docs and made minor tweaks to the --skip_qc and associated options
  • Removed the depreciated uppmax-modules config profile
  • Updated the hebbe config profile to use the new withName syntax too
  • Use new workflow.manifest variables in the pipeline script
  • Updated minimum nextflow version to 0.32.0

Bug Fixes

  • #77: Added back executor = 'local' for the workflow_summary_mqc
  • #95: Check if task.memory is false instead of null
  • #97: Resolved edge-case where numeric sample IDs are parsed as numbers causing some samples to be incorrectly overwritten.

Version 1.0 - 2018-08-20

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.

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!