nf-core/viralrecon v3.0.0 - Waterdog Hibiscus

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 #387
• @Joon-Klaps made their first contribution in #375
• @CaparicaLeo made their first contribution in #483
• @jaimeozaez made their first contribution in #485
• @mashehu made their first contribution in #489
• @cjjossart made their first contribution in #509
• @AnnaNoren made their first contribution in #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 #372
• Remove system exit 1 by @adamrtalbot in #387
• Adding new nf-core subworkflow freyja for weighted variant analysis by @Joon-Klaps in #375
• Important! Template update for nf-core/tools v2.9 by @nf-core-bot in #384
• Remove minia from default assembler by @adamrtalbot in #395
• Fixed conflicts and updated modulels for nf-core/tools version 2.11.1 by @svarona in #408
• Changed primer set to params by @svarona in #393
• Add parameter freyja_depthcutoff by @Joon-Klaps in #412
• Update multiqc & add freyja to MQC by @Joon-Klaps in #413
• Template update for nf-core/tools version 2.12 by @svarona in #416
• Template update for nf-core/tools v2.13.1 by @svarona in #424
• Important! Template update for nf-core/tools v2.13.1 by @nf-core-bot in #421
• Added option to add a custom annotation, clarified multiQC results and fixed issues by @svarona in #401
• 417 allow skipping freyja boot by @Joon-Klaps in #426
• Template update for nf-core/tools version 2.14.1 by @svarona in #430
• Important! Template update for nf-core/tools v2.14.1 by @nf-core-bot in #428
• Enhanced BLAST results filtering by @svarona in #434
• update fastp module by @Joon-Klaps in #438
• fix cardinality when params.bowtie2_index used by @Joon-Klaps in #439
• Important! Template update for nf-core/tools v3.0.2 by @nf-core-bot in #444
• Changed Cutadapt to use nf-core modules by @svarona in #435
• Update nextclade & pangolin modules by @Joon-Klaps in #446
• Patch nf schema - include integer & string as type for sample by @Joon-Klaps in #450
• Fix ch_blast_db to have correct cardinality for blast/blastn by @Joon-Klaps in #452
• Merging 3.1.0 and 3.1.1 template updates by @heuermh in #455
• Important! Template update for nf-core/tools v3.1.1 by @nf-core-bot in #454
• Template update for hackathon nf-core/tools v3.2.0 by @svarona in #464
• Important! Template update for nf-core/tools v3.2.0 by @nf-core-bot in #459
• Update ivar_variants_to_vcf.py: Bug Fixes, Merging Improvements & Refactor by @saramonzon in #469
• resolving redundancies by @CaparicaLeo in #483
• Update local modules versions by @svarona in #486
• Quick fix, test_full.config by @Joon-Klaps in #492
• Remove asciigenome by @svarona in #491
• Added kraken2 to nanopore workflow by @jaimeozaez in #485
• Update modules by @saramonzon in #494
• Switch CI to self hosted runners and update minimal nextflow version by @mashehu in #489
• Important! Template update for nf-core/tools v3.2.1 by @nf-core-bot in #496
• Template update for nf-core/tools v3.3.2. by @svarona in #505
• Important! Template update for nf-core/tools v3.3.2 by @nf-core-bot in #504
• Template update by @svarona in #506
• Use nf-core multiqc module and fixed missing reports by @svarona in #508
• Update multiqc implementation by @Joon-Klaps in #479
• Fix local component structure for #465 by @cjjossart in #509
• Fixed pipelines linting by @svarona in #511
• Some fixes prior to release by @svarona in #518
• Update metro map illumina, Issue #517 by @AnnaNoren in #520
• Template update for nf-core/tools v3.4.1 by @svarona in #533
• Important! Template update for nf-core/tools v3.4.1 by @nf-core-bot in #531
• Important fixes prior to release by @svarona in #523
• Pre-release changes by @svarona in #534
• Added environment.yml files to local modules and added full_aws_test by @svarona in #536
• Fixed freyja channels by @svarona in #537
• fixed software versions for conda by @svarona in #538
• Fix conda snaps by @svarona in #539
• Update artic version and fixed snaps by @svarona in #540
• fixed conda snaps by @svarona in #542
• Dev -> Master for 3.0 release by @svarona in #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 ver...

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.

nf-core/viralrecon v2.5 - Manganese Monkey

[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.

nf-core/viralrecon v2.4.1 - Plastered Magnesium Marmoset

[2.4.1] - 2022-03-01

Enhancements & fixes

• [#288] - --primer_set_version only accepts Integers (incompatible with "4.1" Artic primers set)

nf-core/viralrecon v2.4 - Magnesium Marmoset

[2.4] - 2022-02-22

Enhancements & fixes

• nf-core/tools#1415 - Make --outdir a mandatory parameter
• [#281] - Nanopore medaka processing fails with error if model name, not model file, provided
• [#286] - IVAR_VARIANTS silently failing when FAI index is missing

Parameters

Old parameter	New parameter
	--publish_dir_mode

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.

nf-core/viralrecon v2.3.1 - Patched Copper Coatimundi

[2.3.1] - 2022-02-15

Enhancements & fixes

• [#277] - Misuse of rstrip in make_variants_long_table.py script

Software dependencies

Dependency	Old version	New version
mosdepth	0.3.2	0.3.3
pangolin	3.1.19	3.1.20

nf-core/viralrecon v2.3 - Copper Coatimundi

[2.3] - 2022-02-04

⚠️ Major enhancements

• Please see Major updates in v2.3 for a more detailed list of changes added in this version.
• When using --protocol amplicon, in the previous release, iVar was used for both the variant calling and consensus sequence generation. The pipeline will now perform the variant calling and consensus sequence generation with iVar and BCFTools/BEDTools, respectively.
• Bump minimum Nextflow version from 21.04.0 -> 21.10.3

Enhancements & fixes

• Port pipeline to the updated Nextflow DSL2 syntax adopted on nf-core/modules
• Updated pipeline template to nf-core/tools 2.2
• [#209] - Check that contig in primer BED and genome fasta match
• [#218] - Support for compressed FastQ files for Nanopore data
• [#232] - Remove duplicate variants called by ARTIC ONT pipeline
• [#235] - Nextclade version bump
• [#244] - Fix BCFtools consensus generation and masking
• [#245] - Mpileup file as output
• [#246] - Option to generate consensus with BCFTools / BEDTools using iVar variants
• [#247] - Add strand-bias filtering option and codon fix in consecutive positions in ivar tsv conversion to vcf
• [#248] - New variants reporting table

Parameters

Old parameter	New parameter
	--nextclade_dataset
	--nextclade_dataset_name
	--nextclade_dataset_reference
	--nextclade_dataset_tag
	--skip_consensus_plots
	--skip_variants_long_table
	--consensus_caller
--callers	--variant_caller

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
bcftools	1.11	1.14
blast	2.10.1	2.12.0
bowtie2	2.4.2	2.4.4
cutadapt	3.2	3.5
fastp	0.20.1	0.23.2
kraken2	2.1.1	2.1.2
minia	3.2.4	3.2.6
mosdepth	0.3.1	0.3.2
nanoplot	1.36.1	1.39.0
nextclade		1.10.2
pangolin	3.1.7	3.1.19
picard	2.23.9	2.26.10
python	3.8.3	3.9.5
samtools	1.10	1.14
spades	3.15.2	3.15.3
tabix	0.2.6	1.11
vcflib		1.0.2

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.

nf-core/viralrecon v2.2 - Tin Turtle

[2.2] - 2021-07-29

Enhancements & fixes

• Updated pipeline template to nf-core/tools 2.1
• Remove custom content to render Pangolin report in MultiQC as it was officially added as a module in v1.11
• [#212] - Access to PYCOQC.out is undefined
• [#229] - ARTIC Guppyplex settings for 1200bp ARTIC primers with Nanopore data

nf-core/viralrecon v2.1 - Lead Mink

[2.1] - 2021-06-15

Enhancements & fixes

• Removed workflow to download data from public databases in favour of using nf-core/fetchngs
• Added Pangolin results to MultiQC report
• Added docs about structure of data required for running Nanopore data
• Added docs about using other primer sets for Illumina data
• Added warning to MultiQC report for samples that have no reads after adapter trimming
• Added docs about overwriting default container definitions to use latest versions e.g. Pangolin
• Dashes and spaces in sample names will be converted to underscores to avoid issues when creating the summary metrics
• [#196] - Add mosdepth heatmap to MultiQC report
• [#197] - Output a .tsv comprising the Nextclade and Pangolin results for all samples processed
• [#198] - ASCIIGenome failing during analysis
• [#201] - Conditional include are not expected to work
• [#204] - Memory errors for SNP_EFF step

Parameters

Old parameter	New parameter
--public_data_ids
--skip_sra_fastq_download

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
nextclade_js	0.14.2	0.14.4
pangolin	2.4.2	3.0.5

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.

nf-core/viralrecon v2.0 - Silver Ferret

[2.0] - 2021-05-13

⚠️ Major enhancements

• Pipeline has been re-implemented in Nextflow DSL2
• All software containers are now exclusively obtained from Biocontainers
• Updated minimum Nextflow version to v21.04.0 (see nextflow#572)
• BCFtools and iVar will be run by default for Illumina metagenomics and amplicon data, respectively. However, this behaviour can be customised with the --callers parameter.
• Variant graph processes to call variants relative to the reference genome directly from de novo assemblies have been deprecated and removed
• Variant calling with Varscan 2 has been deprecated and removed due to licensing restrictions
• New tools:
  • Pangolin for lineage analysis
  • Nextclade for clade assignment, mutation calling and consensus sequence quality checks
  • ASCIIGenome for individual variant screenshots with annotation tracks

Other enhancements & fixes

• Illumina and Nanopore runs containing the same 48 samples sequenced on both platforms have been uploaded to the nf-core AWS account for full-sized tests on release
• Initial implementation of a standardised samplesheet JSON schema to use with user interfaces and for validation
• Default human --kraken2_db link has been changed from Zenodo to an AWS S3 bucket for more reliable downloads
• Updated pipeline template to nf-core/tools 1.14
• Optimise MultiQC configuration and input files for faster run-time on huge sample numbers
• [#122] - Single SPAdes command to rule them all
• [#138] - Problem masking the consensus sequence
• [#142] - Unknown method invocation toBytes on String type
• [#169] - ggplot2 error when generating mosdepth amplicon plot with Swift v2 primers
• [#170] - ivar trimming of Swift libraries new offset feature
• [#175] - MultiQC report does not include all the metrics
• [#188] - Add and fix EditorConfig linting in entire pipeline

Parameters

Old parameter	New parameter
--amplicon_bed	--primer_bed
--amplicon_fasta	--primer_fasta
--amplicon_left_suffix	--primer_left_suffix
--amplicon_right_suffix	--primer_right_suffix
--filter_dups	--filter_duplicates
--skip_adapter_trimming	--skip_fastp
--skip_amplicon_trimming	--skip_cutadapt
	--artic_minion_aligner
	--artic_minion_caller
	--artic_minion_medaka_model
	--asciigenome_read_depth
	--asciigenome_window_size
	--blast_db
	--enable_conda
	--fast5_dir
	--fastq_dir
	--ivar_trim_offset
	--kraken2_assembly_host_filter
	--kraken2_variants_host_filter
	--min_barcode_reads
	--min_guppyplex_reads
	--multiqc_title
	--platform
	--primer_set
	--primer_set_version
	--public_data_ids
	--save_trimmed_fail
	--save_unaligned
	--sequencing_summary
	--singularity_pull_docker_container
	--skip_asciigenome
	--skip_bandage
	--skip_consensus
	--skip_ivar_trim
	--skip_nanoplot
	--skip_pangolin
	--skip_pycoqc
	--skip_nextclade
	--skip_sra_fastq_download
	--spades_hmm
	--spades_mode
--cut_mean_quality
--filter_unmapped
--ivar_trim_min_len
--ivar_trim_min_qual
--ivar_trim_window_width
--kraken2_use_ftp
--max_allele_freq
--min_allele_freq
--min_base_qual
--min_coverage
--min_trim_length
--minia_kmer
--mpileup_depth
--name
--qualified_quality_phred
--save_align_intermeds
--save_kraken2_fastq
--save_sra_fastq
--skip_sra
--skip_vg
--unqualified_percent_limit
--varscan2_strand_filter

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.