nf-core/rnaseq v3.10 - Rhodium Rudolph

[3.10] - 2022-12-21

Enhancements & fixes

• Bump minimum Nextflow version from 21.10.3 -> 22.10.1
• Updated pipeline template to nf-core/tools 2.7.2
• [#729] - Add 'auto' option to samplesheet to automatically detect strandedness for samples
• [#889] - Document valid options for --genome parameter
• [#891] - Skip MarkDuplicates when UMIs are used
• [#896] - Remove copyTo call for iGenomes README
• [#897] - Use --skip_preseq by default
• [#898] - Documentation on salmon decoy-aware index creation, gcbias and seqbias
• [#900] - Add --recursive option to fastq_dir_to_samplesheet.py script
• [#902] - check_samplesheet.py script doesn't output optional columns in samplesheet
• [#907] - Add --extra_star_align_args and --extra_salmon_quant_args parameter
• [#912] - Add UMI deduplication before quantification in tube map

Parameters

Old parameter	New parameter
--enable_conda
	--extra_star_align_args
	--extra_salmon_quant_args

NB: Parameter has been updated if both old and new parameter information is present.
NB: Parameter has been added if just the new parameter information is present.
NB: Parameter has been removed if new parameter information isn't present.

Software dependencies

Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own Biocontainer. This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.

Dependency	Old version	New version
bbmap	38.93	39.01
bioconductor-dupradar	1.18.0	1.28.0
bioconductor-summarizedexperiment	1.20.0	1.24.0
bioconductor-tximeta	1.8.0	1.12.0
fq		0.9.1
salmon	1.5.2	1.9.0
samtools	1.15.1	1.16.1

NB: Dependency has been updated if both old and new version information is present.
NB: Dependency has been added if just the new version information is present.
NB: Dependency has been removed if version information isn't present.