nf-core/rnaseq: nf-core/rnaseq v3.3 - Bronze Bear

[3.3] - 2021-07-29 Enhancements & fixes

• Updated pipeline template to nf-core/tools 2.1
• [#556] - Genome index isn't recreated with --additional_fasta unless --star_index false
• [#668] - Salmon quant with UMI-tools does not work
• [#674] - Launch pipeline regex fails

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 samtools 1.10 1.12 stringtie 2.1.4 2.1.7 umi_tools 1.1.1 1.1.2

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.