Skip to content

Commit

Permalink
docs update
Browse files Browse the repository at this point in the history
  • Loading branch information
husensofteng committed Dec 2, 2024
1 parent 7aef2e9 commit 85c1a31
Showing 1 changed file with 4 additions and 2 deletions.
6 changes: 4 additions & 2 deletions docs/kaust.md
Original file line number Diff line number Diff line change
Expand Up @@ -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/<PIPELINE> -profile kaust -r <PIPELINE_VERSION> --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.
Expand Down

0 comments on commit 85c1a31

Please sign in to comment.