sanger-tol/variantcalling v2.0.0 - Qin Shi Huang

Enhancements & fixes

• Update to nf-core template version 3.5.2
• Compatibility with Nextflow's "strict" parser
• Removed the process_vcf sub-workflow, which is now in a new pipeline called variantcomposition.
• When merging reads from multiple runs, order the read files by metadata information to ensure reproducibility.
• Updated all modules, including DeepVariant to 1.10.0 and bcftools to 1.23.1
• Update samplesheet to handle sample in form of specimen/run
• Update outputs for read_mapping and variant_analysis
• Added an option to control PacBio filtering when doing alignments (backported from #153)
• Added an option to pass parameters to DeepVariant (#154)
• DeepVariant resources adjusted for better HPC utilisation (#158)
• Renamed --interval to --intervals to match nf-core/sarek and GATK (#159)

Parameters

NB: Parameter has been updated if both old and new parameter information is present. </br> NB: Parameter has been added if just the new parameter information is present. </br> 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. Only Docker or Singularity containers are supported, conda is not supported.

NB: Dependency has been updated if both old and new version information is present. </br> NB: Dependency has been added if just the new version information is present. </br> NB: Dependency has been removed if version information isn't present.