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Exercise 4: Parallelise OME-Zarr Conversion with Nextflow

In this exercise, we will introduce Nextflow to parallelise the OME-Zarr conversion on cluster. We will be using Nextflow version 25.04.

Nextflow files location

  • Nextflow configuration for the BAND: /scratch/ibSB_workshop_2026/nextflow/nextflow_band.config
  • Nextflow script to convert images: /scratch/ibSB_workshop_2026/nextflow/main_eubi_bridge.nf

Inspect the example conversion script

An example nextflow script is provided at /scratch/ibSB_workshop_2026/nextflow/main_eubi_bridge.nf. Use a text editor available on your BAND desktop to view the script. Refer to Nextflow documentation if you have questions.

Run the Nextflow script

  1. Open a terminal from Application->System Tools->Terminal. This will be used to run Nextflow commands.

  2. Open a second terminal to monitor the cluster queue.

  3. In the second terminal, run the below command to watch jobs submitted by Nextflow. The terminal output refreshes every half seconds.

watch -n .5 squeue -u $USER
  1. In the first terminal, run
nextflow -C /scratch/ibSB_workshop_2026/nextflow/nextflow_band.config run \
    /scratch/ibSB_workshop_2026/nextflow/main_eubi_bridge.nf \
    -profile conda \
    --input_dir /scratch/ngff_workshop/examples/pff \
    --output_dir ~/nf-conversion-results

What happens?

  • -C specifies the configuration file for running Nextflow on BAND
  • -profile conda tells Nextflow to use the preinstalled eubizarr conda environment for dependencies

  • --output_dir sets the directory for conversion results. Nextflow willcreate it automatically.

  • Wait for the run to finish. Once ot finishes, you should see the following completion summary in terminal. nf

Tips:

  • Nextflow will make use the available resources in the BAND cluster.
  • By default, the Nextflow script converts images into OME-Zarr version 0.4. Try search the Eubi-Bridge documentation to try to make it output OME-Zarr version 0.5
  • Always check the content of ~/nf-results to confirm the conversion finished.
  • If you need to re-run the conversion command, remove the contents of ~/nf-conversion-results:
rm -rf ~/nf-conversion-results/*