diff --git a/docs/kaust.md b/docs/kaust.md index eb0bd92d..95365d68 100644 --- a/docs/kaust.md +++ b/docs/kaust.md @@ -22,15 +22,17 @@ module load nextflow Launch the pipeline with `-profile kaust` (one hyphen) to run the workflows using the KAUST profile. This will download and launch the [`kaust.config`](../conf/kaust.config) which has been pre-configured with a setup suitable for the KAUST servers. -It will enable `Nextflow` to manage the pipeline jobs via the `Slurm` job scheduler and `Singularity` to run the tasks. -Using the KAUST profile, `Docker` image(s) containing required software(s) will be downloaded, and converted to `Singularity` image(s) if needed before execution of the pipeline. To avoid downloading same images by multiple users, we provide a singularity `libraryDir` that is configured to use images already downloaded in our central container library. Images missing from our library will be downloaded to your home directory path as defined by `cacheDir`. +It will enable `Nextflow` to manage the pipeline jobs via the `Slurm` job scheduler and `Singularity` to run the tasks. +Using the KAUST profile, `Docker` image(s) containing required software(s) will be downloaded, and converted to `Singularity` image(s) if needed before execution of the pipeline. To avoid downloading same images by multiple users, we provide a singularity `libraryDir` that is configured to use images already downloaded in our central container library. Images missing from our library will be downloaded to your home directory path as defined by `cacheDir`. The KAUST profile makes running the nf-core workflows as simple as: + ```bash module load nextflow # Launch nf-core pipeline with the kaust profile, e.g. for analyzing human data: $ nextflow run nf-core/ -profile kaust -r --genome GRCh38.p14 --samplesheet input.csv [...] ``` + Where `input_csv` contains information about the samples and datafile paths. Remember to use `-bg` to launch `Nextflow` in the background, so that the pipeline doesn't exit if you leave your terminal session.