mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-11-27 10:09:56 +00:00
18 lines
1.5 KiB
Markdown
18 lines
1.5 KiB
Markdown
# nf-core/configs: SAHMRI HPC Configuration
|
|
|
|
All nf-core pipelines have been successfully configured for use on the HPC cluster at [SAHMRI](https://sahmri.org.au/).
|
|
To use, run the pipeline with `-profile sahmri`. This will download and launch the [`sahmri.config`](../conf/sahmri.config) which has been pre-configured
|
|
with a setup suitable for the SAHMRI HPC cluster. Using this profile, either a docker image containing all of the required software will be downloaded,
|
|
and converted to a Singularity image or a Singularity image downloaded directly before execution of the pipeline.
|
|
|
|
The latest version of Nextflow is not installed by default on the SAHMRI HPC cluster. You will need to install it into a directory you have write access to.
|
|
Follow these instructions from the Nextflow documentation.
|
|
|
|
- Install Nextflow : [here](https://www.nextflow.io/docs/latest/getstarted.html#)
|
|
|
|
All of the intermediate files required to run the pipeline will be stored in the `work/` directory. It is recommended to delete this directory after the pipeline
|
|
has finished successfully because it can get quite large, and all of the main output files will be saved in the `results/` directory anyway.
|
|
|
|
> NB: You will need an account to use the SAHMRI HPC cluster in order to run the pipeline. If in doubt contact the ICT Service Desk.
|
|
> NB: Nextflow will need to submit the jobs via SLURM to the SAHMRI HPC cluster and as such the commands above will have to be executed on the login
|
|
> node. If in doubt contact ICT.
|