Nextflow is a highly portable pipeline engine. Please see the official installation guide to learn how to set it up.
This pipeline expects Nextflow version 23.10.1, available here.
This pipeline is set up to work with a range of software provisioning technologies - no need to manually install packages.
You can choose one of the following options:
The pipeline comes with simple pre-set profiles for all of these as described here; if you plan to use this pipeline regularly, consider adding your own custom profile to our central repository to better leverage your available resources.
This pipeline requires locally stored genomes in fasta format. To build these, do:
nextflow run marchoeppner/eutaxpro -profile singularity \\
--build_references \\
--run_name build_refs \\
--outdir /path/to/references
where /path/to/references could be something like /data/pipelines/references or whatever is most appropriate on your system.
If you do not have singularity on your system, you can also specify docker, podman or conda for software provisioning - see the usage information.
The path specified with --outdir can then be given to the pipeline during normal execution as --reference_base. Please note that the build process will create a pipeline-specific subfolder that must not be given as part of the --outdir argument. This pipeline is part of a collection of pipelines that use a shared reference directory and it will choose the appropriate subfolder by itself.
If you run on anything other than a local system, this pipeline requires a site-specific configuration file to be able to talk to your cluster or compute infrastructure. Nextflow supports a wide range of such infrastructures, including Slurm, LSF and SGE - but also Kubernetes and AWS. For more information, see here.
Site-specific config-files for our pipeline ecosystem are stored centrally on github. Please talk to us if you want to add your system.