[2.5] - 2022-07-13 Enhancements & fixes Default Nextclade dataset shipped with the pipeline has been bumped from 2022-01-18T12:00:00Z -> 2022-06-14T12:00:00Z [#234] - Remove replacement of dashes in sample name with underscores [#292] - Filter empty FastQ files after adapter trimming [#303] - New pangolin dbs (4.0.x) not assigning lineages to Sars-CoV-2 samples in MultiQC report correctly [#304] - Re-factor code of ivar_variants_to_vcf script [#306] - Add contig field information in vcf header in ivar_variants_to_vcf and use bcftools sort [#311] - Invalid declaration val medaka_model_string [#316] - Variant calling isn't run when using --skip_asciigenome with metagenomic data [nf-core/rnaseq#764] - Test fails when using GCP due to missing tools in the basic biocontainer Updated pipeline template to nf-core/tools 2.4.1 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 1.2.1 1.2.2 bcftools 1.14 1.15.1 multiqc 1.11 1.13a nanoplot 1.39.0 1.40.0 nextclade 1.10.2 2.2.0 pangolin 3.1.20 4.1.1 picard 2.26.10 2.27.4 quast 5.0.2 5.2.0 samtools 1.14 1.15.1 spades 3.15.3 3.15.4 vcflib 1.0.2 1.0.3 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.