nf-core/viralrecon 3.0.0] - Waterdog Hibiscus - 2025-10-28 Credits Special thanks to the following for their code contributions to the release: Adam Talbot Joon Klaps Sarai Varona Jaime Ozáez Sara Monzon Matthias Hörtenhuber Anna Norén JC Jossart Leo Caparica Michael L Heuer New Contributors @adamrtalbot made their first contribution in https://github.com/nf-core/viralrecon/pull/387 @Joon-Klaps made their first contribution in https://github.com/nf-core/viralrecon/pull/375 @CaparicaLeo made their first contribution in https://github.com/nf-core/viralrecon/pull/483 @jaimeozaez made their first contribution in https://github.com/nf-core/viralrecon/pull/485 @mashehu made their first contribution in https://github.com/nf-core/viralrecon/pull/489 @cjjossart made their first contribution in https://github.com/nf-core/viralrecon/pull/509 @AnnaNoren made their first contribution in https://github.com/nf-core/viralrecon/pull/520 Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form. What's Changed Enhancements & fixes Bump pipeline version to 2.7.0dev by @drpatelh in https://github.com/nf-core/viralrecon/pull/372 Remove system exit 1 by @adamrtalbot in https://github.com/nf-core/viralrecon/pull/387 Adding new nf-core subworkflow freyja for weighted variant analysis by @Joon-Klaps in https://github.com/nf-core/viralrecon/pull/375 Important! Template update for nf-core/tools v2.9 by @nf-core-bot in https://github.com/nf-core/viralrecon/pull/384 Remove minia from default assembler by @adamrtalbot in https://github.com/nf-core/viralrecon/pull/395 Fixed conflicts and updated modulels for nf-core/tools version 2.11.1 by @svarona in https://github.com/nf-core/viralrecon/pull/408 Changed primer set to params by @svarona in https://github.com/nf-core/viralrecon/pull/393 Add parameter freyja_depthcutoff by @Joon-Klaps in https://github.com/nf-core/viralrecon/pull/412 Update multiqc & add freyja to MQC by @Joon-Klaps in https://github.com/nf-core/viralrecon/pull/413 Template update for nf-core/tools version 2.12 by @svarona in https://github.com/nf-core/viralrecon/pull/416 Template update for nf-core/tools v2.13.1 by @svarona in https://github.com/nf-core/viralrecon/pull/424 Important! Template update for nf-core/tools v2.13.1 by @nf-core-bot in https://github.com/nf-core/viralrecon/pull/421 Added option to add a custom annotation, clarified multiQC results and fixed issues by @svarona in https://github.com/nf-core/viralrecon/pull/401 417 allow skipping freyja boot by @Joon-Klaps in https://github.com/nf-core/viralrecon/pull/426 Template update for nf-core/tools version 2.14.1 by @svarona in https://github.com/nf-core/viralrecon/pull/430 Important! Template update for nf-core/tools v2.14.1 by @nf-core-bot in https://github.com/nf-core/viralrecon/pull/428 Enhanced BLAST results filtering by @svarona in https://github.com/nf-core/viralrecon/pull/434 update fastp module by @Joon-Klaps in https://github.com/nf-core/viralrecon/pull/438 fix cardinality when params.bowtie2_index used by @Joon-Klaps in https://github.com/nf-core/viralrecon/pull/439 Important! Template update for nf-core/tools v3.0.2 by @nf-core-bot in https://github.com/nf-core/viralrecon/pull/444 Changed Cutadapt to use nf-core modules by @svarona in https://github.com/nf-core/viralrecon/pull/435 Update nextclade & pangolin modules by @Joon-Klaps in https://github.com/nf-core/viralrecon/pull/446 Patch nf schema - include integer & string as type for sample by @Joon-Klaps in https://github.com/nf-core/viralrecon/pull/450 Fix ch_blast_db to have correct cardinality for blast/blastn by @Joon-Klaps in https://github.com/nf-core/viralrecon/pull/452 Merging 3.1.0 and 3.1.1 template updates by @heuermh in https://github.com/nf-core/viralrecon/pull/455 Important! Template update for nf-core/tools v3.1.1 by @nf-core-bot in https://github.com/nf-core/viralrecon/pull/454 Template update for hackathon nf-core/tools v3.2.0 by @svarona in https://github.com/nf-core/viralrecon/pull/464 Important! Template update for nf-core/tools v3.2.0 by @nf-core-bot in https://github.com/nf-core/viralrecon/pull/459 Update ivar_variants_to_vcf.py: Bug Fixes, Merging Improvements & Refactor by @saramonzon in https://github.com/nf-core/viralrecon/pull/469 resolving redundancies by @CaparicaLeo in https://github.com/nf-core/viralrecon/pull/483 Update local modules versions by @svarona in https://github.com/nf-core/viralrecon/pull/486 Quick fix, test_full.config by @Joon-Klaps in https://github.com/nf-core/viralrecon/pull/492 Remove asciigenome by @svarona in https://github.com/nf-core/viralrecon/pull/491 Added kraken2 to nanopore workflow by @jaimeozaez in https://github.com/nf-core/viralrecon/pull/485 Update modules by @saramonzon in https://github.com/nf-core/viralrecon/pull/494 Switch CI to self hosted runners and update minimal nextflow version by @mashehu in https://github.com/nf-core/viralrecon/pull/489 Important! Template update for nf-core/tools v3.2.1 by @nf-core-bot in https://github.com/nf-core/viralrecon/pull/496 Template update for nf-core/tools v3.3.2. by @svarona in https://github.com/nf-core/viralrecon/pull/505 Important! Template update for nf-core/tools v3.3.2 by @nf-core-bot in https://github.com/nf-core/viralrecon/pull/504 Template update by @svarona in https://github.com/nf-core/viralrecon/pull/506 Use nf-core multiqc module and fixed missing reports by @svarona in https://github.com/nf-core/viralrecon/pull/508 Update multiqc implementation by @Joon-Klaps in https://github.com/nf-core/viralrecon/pull/479 Fix local component structure for #465 by @cjjossart in https://github.com/nf-core/viralrecon/pull/509 Fixed pipelines linting by @svarona in https://github.com/nf-core/viralrecon/pull/511 Some fixes prior to release by @svarona in https://github.com/nf-core/viralrecon/pull/518 Update metro map illumina, Issue #517 by @AnnaNoren in https://github.com/nf-core/viralrecon/pull/520 Template update for nf-core/tools v3.4.1 by @svarona in https://github.com/nf-core/viralrecon/pull/533 Important! Template update for nf-core/tools v3.4.1 by @nf-core-bot in https://github.com/nf-core/viralrecon/pull/531 Important fixes prior to release by @svarona in https://github.com/nf-core/viralrecon/pull/523 Pre-release changes by @svarona in https://github.com/nf-core/viralrecon/pull/534 Added environment.yml files to local modules and added full_aws_test by @svarona in https://github.com/nf-core/viralrecon/pull/536 Fixed freyja channels by @svarona in https://github.com/nf-core/viralrecon/pull/537 fixed software versions for conda by @svarona in https://github.com/nf-core/viralrecon/pull/538 Fix conda snaps by @svarona in https://github.com/nf-core/viralrecon/pull/539 Update artic version and fixed snaps by @svarona in https://github.com/nf-core/viralrecon/pull/540 fixed conda snaps by @svarona in https://github.com/nf-core/viralrecon/pull/542 Dev -> Master for 3.0 release by @svarona in https://github.com/nf-core/viralrecon/pull/535 Parameters | Old parameter | New parameter | | ------------------------------- | ---------------------------- | | | --skip_freyja | | | --freyja_repeats | | | --freyja_db_name | | | --freyja_barcodes | | | --freyja_lineages | | | --skip_freyja_boot | | | --additional_annotation | | | --min_contig_length | | | --min_perc_contig_aligned | | | --skip_noninternal_primers | | | --threeprime_adapters | | | --freyja_depthcutoff | | | --pango_database | | --nextclade_dataset_reference | | | --skip_asciigenome | | | --asciigenome_read_depth | | | --asciigenome_window_size | | | --fast5_dir | | | --artic_minion_caller | | | --artic_minion_aligner | | | --artic_minion_medaka_model | --artic_minion_model_dir | 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 | | ----------------- | ----------- | ----------- | | asciigenome | 1.16.0 | | | artic guppyplex | 1.2.3 | 1.6.2 | | artic minion | 1.2.3 | 1.6.2 | | bandage | 0.8.1 | 0.9.0 | | bcftools | 1.16 | 1.22 | | bedtools | 2.30.0 | 2.31.1 | | biopython | 1.79 | 1.85 | | biostrings | 2.58.0 | 2.66.0 | | blast | 2.13.0 | 2.16.0 | | bowtie2 | 2.4.4 | 2.5.4 | | complexheatmap | 2.6.2 | 2.14 | | coreutils | 9.4 | 9.5 | | cutadapt | 4.2 | 5.0 | | fastp | 0.23.2 | 1.0.1 | | fastqc | 0.11.9 | 0.12.1 | | freyja | | 2.0.1 | | grep | 3.4 | 3.11 | | gzip | | 1.13 | | htslib | 1.20 | 1.22.1 | | ivar | 1.4 | 1.4.4 | | kraken2 | 2.1.2 | 2.1.6 | | lbzip2 | | 2.5 | | matplotlib | 3.5.1 | 3.10.1 | | mosdepth | 0.3.3 | 0.3.11 | | multiqc | 1.14 | 1.31 | | nanoplot | 1.41.0 | 1.46.1 | | nf-schema | | 2.2.1 | | nextclade | 2.12.0 | 3.11.0 | | pangolin | 4.2 | 4.3.1 | | pangolin-data | | 1.32 | | pandas | 1.3.5 | 2.2.3 | | picard | 3.0.0 | 3.4.0 | | python | 3.9.5 | 3.13.2 | | quast | 5.2.0 | 5.3.0 | | regex | 2021.11.10 | 2024.11.6 | | r-base | 4.0.3 | 4.2.0 | | r-ggplot2 | 3.3.3 | 3.5.1 | | r-optparse | 1.6.6 | 1.7.5 | | r-reshape2 | 1.4.4 | 1.4.4 | | r-scales | 1.1.1 | 1.3.0 | | r-sys | 3.4 | 3.4.3 | | r-tidyverse | 1.3.0 | 1.3.2 | | r-viridis | 0.5.1 | 0.6.5 | | samtools | 1.16.1 | 1.22.1 | | scipy | 1.7.3 | 1.15.2 | | sed | 4.7 | 4.9 | | snakemake | 7.30.1 | 8.30.0 | | spades | 3.15.5 | 4.1.0 | | tabix | 1.11 | 1.21 | | Ubuntu | 20.04 | 24.04 | | unicycler | 0.4.8 | 0.5.1 | | vcflib | 1.0.3 | 1.0.14 | 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. Full Changelog: https://github.com/nf-core/viralrecon/compare/2.6.0...3.0.0