Operating System
nf-core/pixelator can be run on any POSIX-compatible x86_64 system, such as Linux or Intel-based macOS.
On Windows, the pipeline can be executed using the WSL2 integration layer.
Software
- To run the pipeline you must have Nextflow installed. Nextflow requires Bash version 3.2 or later, and Java 17 (up to Java 24) to be installed. You can find installation instructions for Nextflow at: https://docs.seqera.io/nextflow/install
- We also require a container runtime to be installed. We recommend using Docker, Singularity, or Apptainer.
Hardware
- Pixelator (and thus the nf-core/pixelator pipeline) only supports x86_64 processors.
- We recommend using a system with at least 32 CPU cores and 512 GB of RAM.
- The pipeline will automatically spread computations across multiple compute nodes if a cluster executor is configured (e.g. SLURM, PBS, LSF, etc.). See the Nextflow documentation for more information on how to configure the pipeline for a specific type of execution environment.
- Disk capacity at runtime should be several times larger than the total size of the FASTQ library files to be processed.
Note that the nf-core community maintain a large number of configuration profiles for different institutional compute clusters. See nf-core/configs for more information. If your cluster is not listed, you can still use the pipeline by creating a custom configuration profile.
If you are working in an environment with slow network storage, you can improve performance by adding the line below to your config file. This setting places data onto a node-local scratch directory as tasks run, and then copies the data back to network storage upon task completion.
process.scratch = true
Read more about this at: https://docs.seqera.io/nextflow/reference/process#scratch