A Reference pipeline to annotate euKaryotes at high resolution
The Hiller Lab at the Senckenberg Research Institute
docs .
pipeline .
us
Note
Requirements: Nextflow ≥ 25.04.6, Docker or Apptainer, Java.
git clone https://github.com/hillerlab/ark.git
cd arkEdit params.json (set relevant options/filters), then:
# Docker
nextflow run main.nf -params-file params.json -profile docker
# Apptainer / Singularity
nextflow run main.nf -params-file params.json -profile apptainerSmoke test:
nextflow run main.nf -profile test,apptainerNote
You can also specify these options directly in params.json.
A helper sh script is provided to run the pipeline on a SLURM cluster. See details below.
Click to expand
Edit the path variables at the top of assets/hpc/ark.sh (cache dir, container image, manifest path), then submit:
sbatch --array=1-<N> ark.shEach array task spawns one Nextflow head job that submits all compute as child SLURM jobs.
PREDICT_ORFS run as SLURM job arrays. Partition routing, array sizes, and resource tiers are documented inline in nextflow.config — edit there to match your cluster.
results/
├── 00_?/ *bed
└── pipeline_info/ timeline, trace, DAG
| File | What |
|---|---|
params.json |
Genome paths, alignment settings, checkpoints — per run |
nextflow.config |
Compute resources, profiles, container, SLURM — rarely |