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Co-authored-by: Pontus Freyhult <pontus_github@soua.net>
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docs/uppmax.md
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@ -13,7 +13,9 @@ Before running the pipeline you will need to either install Nextflow or load it
To use, run the pipeline with `-profile uppmax` (one hyphen). To use, run the pipeline with `-profile uppmax` (one hyphen).
This will download and launch the [`uppmax.config`](../conf/uppmax.config) which has been pre-configured with a setup suitable for the UPPMAX servers. This will download and launch the [`uppmax.config`](../conf/uppmax.config) which has been pre-configured with a setup suitable for the UPPMAX servers.
It will enable Nextflow to manage the pipeline jobs via the Slurm job scheduler. It will enable Nextflow to manage the pipeline jobs via the Slurm job scheduler.
Using this profile, Docker image(s) containing required software(s) will be downloaded, and converted to Singularity image(s) before execution of the pipeline. Using this profile, Docker image(s) containing required software(s) will be downloaded, and converted to Singularity image(s) if needed before execution of the pipeline.
Recent version of Nextflow also support the environment variable `NXF_SINGULARITY_CACHEDIR` which can be used to supply images. Images for some nf-core pipelines are available under `/sw/data/ToolBox/nf-core/` and those can be used by `NXF_SINGULARITY_CACHEDIR=/sw/data/ToolBox/nf-core/; export NXF_SINGULARITY_CACHEDIR`.
In addition to this config profile, you will also need to specify an UPPMAX project id. In addition to this config profile, you will also need to specify an UPPMAX project id.
You can do this with the `--project` flag (two hyphens) when launching nextflow. You can do this with the `--project` flag (two hyphens) when launching nextflow.