Installation¶
Note
The pipeline entrypoint is main.nf, with runtime settings in nextflow.config and profile-specific overrides under conf/.
Prerequisites¶
- Nextflow
>=24.04.0 - Java 17+
- Perl 5
- Python 3 (for
scripts/plot_hydro.py)
Run profiles¶
nextflow run main.nf -profile standard --input data/input.fasta --outdir results
nextflow run main.nf -profile conda --input data/input.fasta --outdir results
nextflow run main.nf -profile hpc --input data/input.fasta --outdir results
Danger
Do not point --outdir to a directory with irreplaceable files, because pipeline publishing uses copy operations to materialize outputs.