From 29dcc160e388bb7d961e67255045fe2b4b27a082 Mon Sep 17 00:00:00 2001 From: Anthony Underwood Date: Thu, 22 Apr 2021 16:04:29 +0100 Subject: [PATCH] Create cambridge.md --- docs/cambridge.md | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 docs/cambridge.md diff --git a/docs/cambridge.md b/docs/cambridge.md new file mode 100644 index 0000000..3f6373e --- /dev/null +++ b/docs/cambridge.md @@ -0,0 +1,17 @@ +# nf-core/configs: Cambridge HPC Configuration +All nf-core pipelines have been successfully configured for use on the Cambridge HPC cluster at the [The University of Cambridge](https://www.cam.ac.uk/). +To use, run the pipeline with `-profile cambridge`. This will download and launch the [`cambridge.config`](../conf/cambridge.config) whichhas been pre-configured +with a setup suitable for the Cambridge 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 Cambridge 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 Cambridge HPC cluster in order to run the pipeline. If in doubt contact IT. +> NB: Nextflow will need to submit the jobs via SLURM to the Cambridge HPC cluster and as such the commands above will have to be executed on one of the login +nodes. If in doubt contact IT.