nf-core/rnaseq version 1.4 "Gray Crocus Dachshund"

Major novel changes include:

• Support for Salmon as an alternative method to STAR and HISAT2

• Several improvements in featureCounts handling of types other than exon. It is possible now to handle nuclearRNAseq data. Nuclear RNA has un-spliced RNA, and the whole transcript, including the introns, needs to be counted, e.g. by specifying --fc_count_type transcript.

• Support for outputting unaligned data to results folders.

• Added options to skip several steps

  • Skip trimming using --skipTrimming
  • Skip BiotypeQC using --skipBiotypeQC
  • Skip Alignment using --skipAlignment to only use pseudo-alignment using Salmon

Documentation updates

• Adjust wording of skipped samples in pipeline output
• Fixed link to guidelines #203
• Add Citation and Quick Start section to README.md
• Add in Documentation of the --gff parameter

Reporting Updates

• Generate MultiQC plots in the results directory #200
• Get MultiQC to save plots as standalone files
• Get MultiQC to write out the software versions in a .csv file #185
• Use file instead of new File to create pipeline_report.{html,txt} files, and properly create subfolders

Pipeline enhancements & fixes

• Restore SummarizedExperimment object creation in the salmon_merge process avoiding increasing memory with sample size.
• Fix sample names in feature counts and dupRadar to remove suffixes added in other processes
• Removed genebody_coverage process #195
• Implemented Pearsons correlation instead of Euclidean distance #146
• Add --stringTieIgnoreGTF parameter #206
• Removed unused stringtie channels for MultiQC
• Integrate changes in nf-core/tools v1.6 template which resolved #90
• Moved process convertGFFtoGTF before makeSTARindex #215
• Change all boolean parameters from snake_case to camelCase and vice versa for value parameters
• Add SM ReadGroup info for QualiMap compatibility#238
• Obtain edgeR + dupRadar version information #198 and #112
• Add --gencode option for compatibility of Salmon and featureCounts biotypes with GENCODE gene annotations
• Added functionality to accept compressed reference data in the pipeline
• Check that gtf features are on chromosomes that exist in the genome fasta file #274
• Maintain all gff features upon gtf conversion (keeps gene_biotype or gene_type to make featureCounts happy)
• Add SortMeRNA as an optional step to allow rRNA removal #280
• Minimal adjustment of memory and CPU constraints for clusters with locked memory / CPU relation
• Cleaned up usage, parameters.settings.json and the nextflow.config

Dependency Updates

• Dependency list is now sorted appropriately
• Force matplotlib=3.0.3

Updated Packages

• Picard 2.20.0 -> 2.21.1
• bioconductor-dupradar 1.12.1 -> 1.14.0
• bioconductor-edger 3.24.3 -> 3.26.5
• gffread 0.9.12 -> 0.11.4
• trim-galore 0.6.1 -> 0.6.4
• gffread 0.9.12 -> 0.11.4
• rseqc 3.0.0 -> 3.0.1
• R-Base 3.5 -> 3.6.1

Added / Removed Packages

• Dropped CSVtk in favor of Unix's simple cut and paste utilities
• Added Salmon 0.14.2
• Added TXIMeta 1.2.2
• Added SummarizedExperiment 1.14.0
• Added SortMeRNA 2.1b
• Add tximport and summarizedexperiment dependency #171
• Add Qualimap dependency #202

nf-core/rnaseq 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

nf-core/rnaseq version 1.2

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

nf-core/rnaseq version 1.1

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

Software updates

• FastQC 0.11.7 > 0.11.8
• STAR 2.6.1a > 2.6.1b
• Picard 2.18.11 > 2.18.14
• Deeptools 3.1.1 > 3.1.4

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.

nf-core/rnaseq version 1.0

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!