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nf-core/rnaseq: Changelog

Version 1.4.2

  • Minor version release for keeping Git History in sync
  • No changes with respect to 1.4.1 on pipeline level

Version 1.4.1

Major novel changes include:

  • Update igenomes.config with NCBI GRCh38 and most recent UCSC genomes
  • Set autoMounts = true by default for singularity profile

Pipeline enhancements & fixes

  • Fixed parameter warnings #316 and 318
  • Fixed #307 - Confusing Info Printout about GFF and GTF

Version 1.4

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

Version 1.3 - 2019-03-26

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
  • Add option for Trimming NextSeq data properly (@jburos work)

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
  • Use file instead of new File to create the pipeline_report.{html,txt} files to avoid creating local directories when outputting to AWS S3 folders

Dependency Updates

  • RSeQC 2.6.4 -> 3.0.0
  • Picard 2.18.15 -> 2.20.0
  • r-data.table 1.11.4 -> 1.12.2
  • bioconductor-edger 3.24.1 -> 3.24.3
  • r-markdown 0.8 -> 0.9
  • csvtk 0.15.0 -> 0.17.0
  • stringtie 1.3.4 -> 1.3.6
  • subread 1.6.2 -> 1.6.4
  • gffread 0.9.9 -> 0.9.12
  • multiqc 1.6 -> 1.7
  • deeptools 3.2.0 -> 3.2.1
  • trim-galore 0.5.0 -> 0.6.1
  • qualimap 2.2.2b
  • matplotlib 3.0.3
  • r-base 3.5.1

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!