This is not a full release. Please note that some things may not work as intended yet. Specifically: While most processes will use containers or conda environments as requested, the final reporting steps currently require locally:
- ruby v >= 3.0
- gems: json, rubyXL
This will be corrected towards the full 1.0 release, at which point the pipeline will be fully platform-independent and self-contained.
This pipeline requires locally stored genomes in fasta format. To build these, do:
nextflow run marchoeppner/gmo-check -profile standard,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 (gmo-check) that must not be given as part of the --outdir argument. Gmo-check 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