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