microeuk-nf is a Nextflow workflow for ONT and PacBio HiFi metagenomes that contain microbial eukaryotes, bacteria, archaea, and viruses. It performs read QC, assembly, binning, independent quality and taxonomy analyses, and optional gene calling and functional annotation. Quality, taxonomy, RNA, and protein evidence determine the gene-calling branches. The workflow writes a validated SQLite catalog, native visualization bundles, an executed notebook, and an HTML report.
Candidate routes guide downstream analysis; they are not final taxonomy or accepted MAG labels.
The publication name is microeuk-nf. Established internal identifiers remain
protist-meta-nf for the Nextflow and Pixi workspaces, protist-meta for the
CLI, protist_meta for the Python package, and protist-meta.sqlite for the
catalog filename.
git clone git@github.com:nelli-team/microeuk-nf.git
cd microeuk-nfThe clone is not a standalone full installation. conf/databases.yaml points to
local reference databases, sibling Pixi workspaces for CheckM1, CheckM2,
GTDB-Tk, Symclatron, geNomad, and CheckV, and application workspaces for
CheckEUK, GVClass, and SSUextract. Configure those paths for the target Dori
filesystem before a full run. The repository installers also retain fixed local
eggNOG and InterProScan setup paths.
Follow Run and resume on Dori for the ordered
environment setup and submission commands. Copy
data/samples.example.tsv to a file of your choice,
edit its single row, and keep all 13 columns. Input paths are resolved relative
to that copied sample sheet.
Both optional stages are enabled by default in full mode. Add
--skip-annotation to the allocation launcher to retain gene models without
functional annotation, or --skip-gene-calling to omit both stages. The catalog
and report record the disabled stages and their reasons.
- Source-scoped validation records accepted runs and scientific limits.
- Scientific design explains the evidence and routing rules.
- Input and dependency contract defines the sample fields and local dependency boundary.
- Report API describes catalog reporting and interpretation.
Generated run outputs, validation receipts, and working notes are local artifacts excluded from Git. The repository contains the reviewed source and documentation; it does not claim a hosted documentation site.