From ce4b0373facc5841e0ea0907b4530f9ce5ff6a4a Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Sun, 6 Jan 2019 15:35:26 +0100 Subject: [PATCH] Add in UZH --- docs/uzh.md | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 docs/uzh.md diff --git a/docs/uzh.md b/docs/uzh.md new file mode 100644 index 0000000..08a81d7 --- /dev/null +++ b/docs/uzh.md @@ -0,0 +1,15 @@ +# nf-core/configs: UZH Configuration + +All nf-core pipelines have been successfully configured for use on the UZH cluster at the insert institution here. + +To use, run the pipeline with `-profile UZH`. This will download and launch the [`uzh.config`](../conf/uzh.config) which has been pre-configured with a setup suitable for the UZH cluster. Using this profile, Nextflow will download a singularity image with all of the required software before execution of the pipeline. + +## Example command for nf-core/atacseq +nextflow run nf-core/atacseq -profile PROFILE --genome GRCh37 --design /path/to/design.csv --email test.user@crick.ac.uk +``` + +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 HPC cluster UZH in order to run the pipeline. If in doubt contact IT. + +>NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT.