nf-core/viralrecon: nf-core/viralrecon v2.6.0 - Rhodium Raccoon

[2.6.0] - 2023-03-23 Credits Special thanks to the following for their code contributions to the release: Friederike Hanssen Hugo Tavares James Fellows Yates Jessica Wu Matthew Wells Maxime Garcia Phil Ewels Sara Monzón Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form. Enhancements & fixes [#297] - Add tube map for pipeline [#316] - Variant calling isn't run when using --skip_asciigenome with metagenomic data [#317] - ivar_variants_to_vcf: Ignore lines without annotation in ivar tsv file [#320] - Pipeline fails at email step: Failed to invoke workflow.onComplete event handler [#321] - ivar_variants_to_vcf script: Duplicated positions in tsv file due to overlapping annotations [#334] - Longshot thread 'main' panicked at 'assertion failed: p <= 0.0' error [#341] - artic/minion and artic/guppyplex: Update module version 1.2.2 -> 1.2.3 [#348] - Document full parameters of iVar consensus [#349] - ERROR in Script plasmidID [#356] - Add NEB SARS-CoV-2 primers [#368] - Incorrect depth from ivar variants reported in variants long table Updated pipeline template to nf-core/tools 2.7.2 Add tower.yml for Report rendering in Nextflow Tower Use --skip_plasmidid by default Parameters Old parameter New parameter --tracedir 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 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 artic 1.2.2 1.2.3 bcftools 1.51.1 1.16 blast 2.12.0 2.13.0 cutadapt 3.5 4.2 ivar 1.3.1 1.4 multiqc 1.13a 1.14 nanoplot 1.40.0 1.41.0 nextclade 2.2.0 2.12.0 pangolin 4.1.1 4.2 picard 2.27.4 3.0.0 samtools 1.15.1 1.16.1 spades 3.15.4 3.15.5 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 new version information isn't present