v2026.8.13
Lungfish 2026.8.13
Channel: Stable
Previous versioned release: v2026.8.12
Stable baseline: v2026.8.7
Dependency set: 2026.2
Lungfish 2026.8.13 promotes the work validated across previews 2026.8.8 through
2026.8.12 to the stable channel. This release improves large metagenomics
projects, deep alignment viewing, FASTQ processing, external-volume workflow
execution, and consensus generation. It also lets Preview and Stable installs
live side by side as Lungfish Preview.app and Lungfish.app.
Included preview releases
- v2026.8.8
- v2026.8.9
- v2026.8.10
- v2026.8.11
- v2026.8.12
Highlights
Metagenomics projects use less storage and preserve clearer provenance
Kraken2 classifications now reference durable imported FASTQ inputs instead of
copying them into each analysis. Bracken outputs and degraded negative-control
profiles are represented accurately in results and provenance. Taxon search,
Bracken count columns, sample-correct BLAST verification, and transactional
FASTQ/FASTA extraction improve review of multi-sample classifications.
Deep alignment viewing remains responsive and scientifically complete
Alignment viewers open at the full contig, show reference differences at every
read-visible zoom, and pack reads off the main thread. A visible-read budget
keeps extreme-depth samples interactive without changing depth, coverage, or
consensus calculations. Detached viewers restore read hit-testing and visible
interval selections, transient evidence state clears promptly, and failed
depth queries retry rather than leaving a permanently blank plot.
Coverage tracks can now use linear, log10, or square-root display scaling.
The selected scale changes presentation only; underlying depth values and
exports remain unchanged.
FASTQ processing is faster and more predictable
Read Processing adds a BBTools entropy-based low-complexity filter with GUI and
CLI parity. Operations preserve gzip compression where the underlying tool can
write it safely, report live per-sample phases, and use seqkit aggregates plus
sampled distributions for fast post-operation statistics. Streaming FASTQ and
gzip readers now apply backpressure and bounded child-process teardown, and
BBTools heap sizing leaves memory available for concurrent work.
Workflows behave correctly across local and external volumes
Nextflow scratch placement is selected by probing real file locks and native
extended attributes. APFS/HFS+ project volumes can host scratch locally, while
exFAT, FAT, and incompatible network volumes use local scratch to avoid
AppleDouble sidecar failures. Empty stderr no longer hides useful pipeline
errors because the stdout tail is used as a fallback.
Consensus, controls, and application behavior
Whole-contig consensus generation now accepts the bare FASTA headers emitted
by samtools consensus, including contig names that themselves contain colons.
Every slider has direct numeric entry with range clamping and step snapping.
Dock activation restores minimized windows, scrolling follows macOS direction
settings, read tracks remain clipped to their viewport, and stale overlays or
deleted results no longer remain displayed.
Stable and Preview installations
The stable DMG contains Lungfish.app; preview DMGs contain
Lungfish Preview.app. Both may be installed in /Applications at once.
They intentionally retain the same bundle identifier for Sparkle compatibility,
while their filenames, visible names, release-channel metadata, and feed URLs
remain channel-specific.
Storage and migration notes
Existing classification analysis folders are not rewritten. Older
.lungfish-provenance/intermediates/classification-inputs copies may be removed
manually after confirming their recorded replay commands are no longer needed.
Legacy Bracken output names remain readable. Existing preview installations
continue updating in place; installing a current preview DMG is what establishes
the side-by-side Lungfish Preview.app filename.
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_0self-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 the stable baseline.
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.