[1.1.0] – Hebridean Black - [2023-03-16] Enhancements & fixes Bump minimum Nextflow version from 22.04.0 -> 22.10.1 Updated pipeline template to nf-core/tools 2.7.1 Added nf-core modules to replace most local modules Added improved resource settings Added support for unit and full tests on Sanger HPC via Nextflow Tower Added all unit test data on a S3 bucket Added statistics subworkflow functionality to the alignment subworkflows Removed support for iGenomes Removed samtools faidx and minimap index module, it now happens on the fly Parameters Old parameter New parameter --enable_conda --minimap2_index --samtools_index 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 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 minimap2 2.21 2.24 samtools 1.15 and 1.15.1 1.14 and 1.16.1 multiqc 1.11 and 1.12 1.13 bam2fastx 1.3.1 pbbam 2.1.0 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.