nf-core/rnaseq 1.4

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

on GitHub

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