diff --git a/docs/uppmax.md b/docs/uppmax.md index 1cf8690..9057b2a 100644 --- a/docs/uppmax.md +++ b/docs/uppmax.md @@ -13,9 +13,10 @@ Before running the pipeline you will need to either install Nextflow or load it 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. 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) if needed 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`. +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. You can do this with the `--project` flag (two hyphens) when launching nextflow.