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v2026.8.14

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@dhoconno dhoconno released this 30 Aug 00:21
v2026.8.14
3496019

Lungfish 2026.8.14

Channel: Preview

Previous versioned release: v2026.8.13

Stable baseline: v2026.8.13

Dependency set: 2026.2

Lungfish 2026.8.14 is a preview release focused on reliable MiSeq genotype
publication and compatibility with legacy IPD-MHC reference identifiers.

Preview builds are under rapid iterative development. Features may be incomplete, change quickly, or require additional feedback.

Highlights

Legacy IPD-MHC references publish with their original identifiers

FASTA-only reference bundles can now resolve structured legacy IPD-MHC sequence
identifiers, including allele aliases and group labels used by older macaque MHC
datasets. Lungfish preserves those identifiers as display names while deriving
the correct MHC locus for exact joins between genotype calls and reference rows.
Malformed identifiers remain rejected instead of being interpreted loosely.

MiSeq genotype publication accepts platform-native CSV line endings

Scientific-artifact and reviewable-row publication now normalize CRLF and CR
line endings before parsing genotype and sample-summary CSV files. This prevents
valid producer output—including rows where passed alignment and unique-read
counts are equal—from being lost or misread during publication.

Genotype CSV headers are validated before indexing. Empty or duplicate column
names now produce an explicit malformed-CSV error rather than an ambiguous
dictionary failure.

Known issues

  • The 20260626 Kraken2 indexes display taxid 3418604 as
    Betacoronavirus pandemicum; identifiers are unchanged.
  • The Apple Silicon bioconda Bracken compatibility package lacks a usable
    driver. Fresh installs receive the managed Bracken 3.1 source overlay, while
    existing working environments are preserved.
  • bioconda::bwa-mem2=2.3=hda5e58c_0 self-reports 2.2.1 because of an upstream
    packaging defect; Lungfish verifies the package identity from conda metadata.

Dependency versions

Dependency set 2026.2 (2026-08-18) is unchanged from v2026.8.13.

Core managed tools: Nextflow 26.04.6, Snakemake 9.25.2, BBTools 40.02,
fastp 1.3.6, deacon 0.16.0, samtools 1.24, bcftools 1.24, htslib 1.24,
seqkit 2.13.0, cutadapt 5.2, Trim Galore 2.3.0, vsearch 2.31.0, pigz 2.8,
SRA Tools 3.4.1, UCSC bedGraphToBigWig 482, pysam 0.24.0, and openpyxl 3.1.5.

Plugin tools: minimap2 2.31, bwa-mem2 2.3, Bowtie 2 2.5.5, Savont 0.6.3,
BLAST 2.16.0, LoFreq 2.1.5, iVar 1.4.4, Medaka 2.2.2, Clair3 2.0.2,
GATK 4.6.2.0, WhatsHap 2.3, SPAdes 4.3.0, MEGAHIT 1.2.9, SKESA 2.5.1,
Flye 2.9.6, hifiasm 0.25.0, MAFFT 7.526, IQ-TREE 3.1.3, Kraken2 2.17.1,
Bracken 3.1 source overlay, EsViritu 1.3.3, RiboDetector 0.3.3, and Freyja 2.0.3.

Pipelines and data: TaxTriage v3.3.8 at revision
e10bfebda32a62711f38a4e23ab03b61725a9675, nf-core/viralrecon 3.0.0,
Kraken2 indexes 20260626 (plus EukPathDB 20230407), EsViritu viral database
v3.2.4, NCBI taxonomy 2025-03, human scrubber 20260706v2, deacon panhuman
panhuman-1, and ribokmers bbmap-ribokmers-k31w15. The bootstrap is
micromamba 2.9.0-0.

Swift packages: Sparkle 2.9.6, swift-argument-parser 1.8.2,
swift-protobuf 1.35.0, swift-nio 2.101.3, swift-nio-ssl 2.37.2,
swift-nio-http2 1.45.0, grpc-swift 1.27.5, async-http-client 1.36.0,
swift-collections 1.6.0, swift-crypto 3.15.1, swift-certificates 1.19.4,
swift-system 1.8.1, swift-service-lifecycle 2.12.0, containerization 0.24.5,
zstd 1.5.7, and ViewInspector 0.10.3. Remaining transitive pins are recorded
exactly in Package.resolved.

Assets 3
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