nf-core/rnaseq v3.9 - Niobium Nightingale

[3.9] - 2022-09-30

Enhancements & fixes

• [#746] - Add tin.py output to MultiQC report
• [#841] - Turn --deseq2_vst on by default
• [#853] - Pipeline fails at email step: Failed to invoke workflow.onComplete event handler
• [#857] - Missing parameter required by StringTie if using STAR as aligner
• [#862] - Filter samples that have no reads after trimming
• [#864] - Pre-process transcripts fasta when using --gencode
• Expose additional arguments to UMI-tools as pipeline params: --umitools_bc_pattern2 is required if the UMI is located on read 2. --umitools_umi_separator will often be needed in conjunction with --skip_umi_extract as most other tools such as Illumina's BCL Convert use a colon instead of an underscore to separate the UMIs. The --umitools_grouping_method allows to fine-tune handling of similar but non-identical UMIs.
• Updated pipeline template to nf-core/tools 2.5.1

Parameters

Old parameter	New parameter
	--umitools_bc_pattern2
	--umitools_umi_separator
	--umitools_grouping_method

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
hisat2	2.2.0	2.2.1
multiqc	1.11	1.13
picard	2.26.10	2.27.4

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.