Added

• Template update for nf-core/tools v3.5.2 (#270) (by @Joon-Klaps)
• Modules update to latest nf-core versions (#271) (by @Joon-Klaps)
• Update local modules to use topics (#272) (by @Joon-Klaps)
• Add better output file descriptions for prokka #274 (by @Joon-Klaps)
• Better item descriptors (it -> [it[0], it[1] to meta, fasta , _foo -> [meta,fasta]) for better readability (#265) (by @Joon-Klaps)
• Include the new parameter --transpose_overview_tables , fixes #220 (#275) (by @Joon-Klaps)
• Bump version from dev to 1.1.1 for release (#277) (by @Joon-Klaps)

Fixed

• Follow the rules of strict syntax health #265 (by @Joon-Klaps)
• Moved the module specifics from base.config to modules.config (#265)
• Fix bug from regex in input schema still allowing underscores in sample and group names (#269) - (by @Joon-Klaps)

Dependencies

Parameters

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.

v1.1.0 - 2026-01-23

Added

• Add subworkflow tests of fasta_fastq_clust and fasta_contig_clust #253 (by @Joon-Klaps)
• Add subworkflow tests for preprocessing_illumina and fastq_fastqc_umitools_trimmomatic #255 (by @Joon-Klaps)

Fixed

• Fix memory issues for network_cluster #105 by switching to Clusty #251 (by @Joon-Klaps)
• Improve memory efficiency and speed of FASTA sequence extraction #252 (by @Joon-Klaps)
• Fix bug of clusty not handling single genome distance files well #253 (by @Joon-Klaps)
• Fix reported trimmomatic bug #254 ‘no such variable “trim_read_count”’ #255 (by @Joon-Klaps)
• Fix descrepancy of documentation and actual arguments #256 (by @Joon-Klaps)
• Fix performance issues with extract_cluster.py for large datasets #259 (by @Joon-Klaps)

Dependencies

v1.0.1 - 2025-12-03

Added

• Update modules (#237) (by @Joon-Klaps)

Fixed

• Template merge from nf-core/tools v3.5.1 (#236) (by @Joon-Klaps)
• Fix bug with numeric sample ids in custom_multiqc.py module (#243) (by @Joon-Klaps)
• Fix runtime environment migration of network_cluster from custom docker repo to seqera containers (#247) (by @Joon-Klaps)

Dependencies

v1.0.0 - 2025-11-04

Initial release of nf-core/viralmetagenome, created with the nf-core template.

Added

• Add argument to control the maximum mpileup depth in custom_mpileup.py script (#176) (by @Joon-Klaps)
• Removing redundant samtools_sort after BAM_DEDUPLICATE (#177) (by @Joon-Klaps)
• Removing seqkit replace and move logic to blast_filter.py (#178) (by @Joon-Klaps)
• Giving Kaiju more memory (#179) (by @Joon-Klaps)
• Add option for sample merging based on group column in samplesheet (#180) (by @Joon-Klaps)
• Creating testdatasets using nf-core repo (#183) (by @Joon-Klaps)
• Add option to annotate snps with Snpeff for mapping constraint route (#186) (by @Joon-Klaps)
• Add nf-tests for test profile (#189) (by @Joon-Klaps)
• Update docs (#200) (by @Joon-Klaps)
• Template update for nf-core/tools v3.3.2 (#202) (by @Joon-Klaps)
• Add option for local desktop configuration profile (#227) (by @Joon-Klaps)
• Added option to blacklist certain NCBI accessions (--blacklist) from reference pool (--reference_pool) (#228) (by @Joon-Klaps)
• Add support for both string and integer inputs in samplesheets through validation.lentientMode = true (#230) (by @Joon-Klaps)

Fixed

• Fix local module ivar_variants_to_vcf to handle empty tsv files (#197) (by @Joon-Klaps)
• Migrate lib dir functions to utils_nfcore_viralmetagenome_pipeline (#194) (by @Joon-Klaps)
• Fix inconsistent dependency versions across modules (#208) (by @Joon-Klaps)
• Fix conda issue unrecognized arguments: –mkdir (#210) (by @Joon-Klaps)
• Fix writing no sequence for select_reference.py to the first reference of the multifasta (#214) (by @Joon-Klaps)
• Fix main language detection to ignore generated files (#224) (by @Joon-Klaps)

Deprecated

• Refactor params.skip_annotation to params.skip_consensus_annotation(#181) (by @Joon-Klaps)
• Deprecate params.skip_nocov_to_reference (#212) (by @Joon-Klaps)
• Deprecate BWAMEM as mapping tool (#212) (by @Joon-Klaps)

Second release of the viralgenie pipeline. Focusing on user experience and bug fixes.

Enhancement

• Set default umitools dedup strategy to cluster (#126)
• Include both krakenreport &nodes.dmp in taxonomy filtering (#128)
• Add Sspace indiv to each assembler seperatly (#132)
• Add read & contig decomplexification using prinseq++ (#133)
• Add option to filter contig clusters based on cumulative read coverage (#138)
• Reffurbish mqc implementation (#139)
• Adding mash-screen output to result table (#140)
• Add logic to allow samples with no reference hits to be analysed (#141)
• Add visualisation for hybrid scaffold (#143)
• Add new module to inculde custom mpileup-vcf file for intra-host analyses (#151)
• Update docs (#150)
• Make custom-mpileup.py postion 1 index based and not 0 index to follow bcftools (#153)
• Update docs for more streamlined docs & figures (#154)
• Add column in custom mpileup - Shannon entropy (#156)
• Constrain -> Constraint & further python script debugging (#161)
• include empty samples in multiqc sample overview (#162)
• Include samtools stats pre dedup & post dedup in overview tables (#163)
• adding prokka for gene detection & annotation (#165)

Fixed

• OOM with longer contigs for nocov_to_reference, uses more RAM now (#125)
• fixing null output from global prefix (#147)
• Fix empty filtered clusters (#148)
• Fixing missing columns from general stats & add general stats sample filtering (#149)
• process.shell template fix (#157) - see also nf-core/tools #3416

Parameters

• DEPRECATED- New parameter mmseqs_cluster_mode default to 0 (#130)
• Refactor module arguments to pipeline arguments (#166)

Initial pre-release with core functionalities.

What’s Changed

• Update versions by @Joon-Klaps in #117
• combine multiple functions of preclustering into one by @Joon-Klaps in #111
• 102 autodetect paired end by @Joon-Klaps in #109
• 65 select best ref by @Joon-Klaps in #107
• 105 out of memory during network cluster process on unclassified taxa by @Joon-Klaps in #106
• Continue making docs by @Joon-Klaps in #104
• 61 update docs make release by @Joon-Klaps in #103
• Handling singletons by @Joon-Klaps in #101
• Include bwamem mapper + multifasta support + virosaurs annotation by @Joon-Klaps in #100
• Fixing dev by @Joon-Klaps in #99
• Revert “49 samplesheet mapping constrains” by @Joon-Klaps in #97
• Add clean_output_on_error parameter and implement directory deletion … by @Joon-Klaps in #94
• Modules update by @Joon-Klaps in #92
• Annotate with mmseqs instead of blast by @Joon-Klaps in #91
• Making hybrid scaffold optional by @Joon-Klaps in #89
• Alignment free deduplication by @Joon-Klaps in #87
• template v2.12 by @Joon-Klaps in #86
• Add annotation of final contigs by @Joon-Klaps in #83
• Add “subject title” column to blast_df and update ext.args in modules… by @Joon-Klaps in #82
• 67 multiqc report for quast include assemblers by @Joon-Klaps in #81
• Joon klaps/include krona report by @Joon-Klaps in #79
• Add seqkit/replace module for string replacement in sequences by @Joon-Klaps in #77
• Add changelog configuration bot v0.1dev by @Joon-Klaps in #76
• Joon klaps/mpileup calling without reference by @Joon-Klaps in #71
• Add global prefix to publishDir paths by @Joon-Klaps in #70
• Add fastp deduplication option and accuracy parameter by @Joon-Klaps in #69
• 49 samplesheet mapping constrains by @Joon-Klaps in #60
• Update input parameters in make_bed_mask.nf, main.nf, and mem.nf by @Joon-Klaps in #59
• module version bump by @Joon-Klaps in #54
• Template update by @Joon-Klaps in #53