nf-core/rnaseq v3.12.0 - Osmium Octopus

[3.12.0] - 2023-06-02

Credits

Special thanks to the following for their contributions to the release:

• Adam Talbot
• Esha Joshi
• Ghepardo
• Matthias Zepper
• Maxime Garcia
• Rob Syme

Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.

Enhancements & fixes

• [#1011] - FastQ files from UMI-tools not being passed to fastp
• [#1018] - Ability to skip both alignment and pseudo-alignment to only run pre-processing QC steps.
• PR #1016 - Updated pipeline template to nf-core/tools 2.8
• PR #1025 - Add public_aws_ecr.config to source mulled containers when using public.ecr.aws Docker Biocontainer registry
• PR #1038 - Updated error log for count values when supplying --additional_fasta
• PR #1042 - revert samtools_sort modules to no memory assignement

Parameters

Old parameter	New parameter
	--skip_pseudo_alignment

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

Dependency	Old version	New version
fastp	0.23.2	0.23.4
samtools	1.16.1	1.17

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 new version information isn't present.