MPUSP/snakemake-ont-basecalling
A Snakemake workflow for basecalling and demultiplexing of Oxford Nanopore data using Dorado.
Overview
Testing:
Last update: 2026-03-24
Latest release: v1.6.0
Topics: basecalling cluster dorado nanopore-sequencing oxford-nanopore parallel-computing slurm snakemake snakemake-workflow
Configuration
The following configuration details are extracted from the config's README file.
Running the workflow
Input data
This workflow requires pod5 input data. These input files are supplied to the workflow using a mandatory runs table linked in the config.yml file (default: .test/config/runs.csv). Each row in the runs table corresponds to a single run, for which all pod5 files are provided via a data_folder column. Multiple runs can be defined in the table.
The runs table has the following layout:
| run_id | data_folder | basecalling_model | barcode_kit |
|---|---|---|---|
| MK1C_run_01 | ".test/data" | dna_r10.4.1_e8.2_400bps_sup@v5.0.0 | SQK-PCB114-24 |
Execution
To define rule specific resources like GPU usage, configuration profiles will be used. See snakemake docs on profiles for more information. A default profile for local testing and a slurm specific cluster profile is provided with this workflow.
To run the workflow from command line, change to the working directory and activate the conda environment.
cd snakemake-ont-basecalling
conda activate snakemake-ont-basecalling
Adjust options in the default config file config/config.yml.
Before running the entire workflow, perform a dry run using:
snakemake --cores 3 --sdm conda --directory .test --dry-run
To run the workflow with test files using conda:
snakemake --cores 3 --sdm conda --directory .test
To run the workflow with test files using conda and apptainer, set the dorado path to /share/resources/dorado-<version>-linux-x64/bin/dorado and make it available for apptainer using bind:
snakemake --cores 3 --sdm conda apptainer --directory .test --apptainer-args "--bind ../resources:/share/resources"
To run the workflow with test files on a slurm cluster, adjust the slurm-specific profile workflow/profiles/slurm/config.yaml file and run:
snakemake --cores 3 --sdm conda --workflow-profile workflow/profiles/slurm/ --directory .test
Note: It is recommended to start the snakemake pipeline on the cluster using a session multiplexer like screen or tmux.