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

[3.3] - 2021-07-29 Enhancements &amp; 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 <code>samtools</code> 1.10 1.12 <code>stringtie</code> 2.1.4 2.1.7 <code>umi_tools</code> 1.1.1 1.1.2 <strong>NB:</strong> Dependency has been <strong>updated</strong> if both old and new version information is present. <strong>NB:</strong> Dependency has been <strong>added</strong> if just the new version information is present. <strong>NB:</strong> Dependency has been <strong>removed</strong> if version information isn't present.