Enhancements & fixes Upgrade to the version 3.5.2 of the nf-core template Compatible with Nextflow's strict parser All modules updated The directories comply with Tree of Life's canonical directory structure. New logo, with Sanger colours Pipeline diagram, thanks to nf-metro Software dependencies Note, since the pipeline is 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 bgzip 1.20 1.21 MultiQC 1.20 Python 3.9.1 samtools 1.21 1.23.1 tabix 1.20 1.21 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.

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