From dba3fb4c1d51996b02c0451222937a2d06fd0e41 Mon Sep 17 00:00:00 2001 From: Nathan Watson-Haigh Date: Sun, 13 Mar 2022 00:05:34 +1030 Subject: [PATCH] Added SAHMRI HPC profile docs --- docs/sahmri.md | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/docs/sahmri.md b/docs/sahmri.md index e69de29..4ef285e 100644 --- a/docs/sahmri.md +++ b/docs/sahmri.md @@ -0,0 +1,18 @@ +# 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.