diff --git a/README.md b/README.md index 68beab2..6daff2a 100644 --- a/README.md +++ b/README.md @@ -100,6 +100,7 @@ Currently documentation is available for the following systems: * [BI](docs/bi.md) * [BINAC](docs/binac.md) * [BIOHPC_GEN](docs/biohpc_gen.md) +* [CAMBRIDGE](docs/cambridge.md) * [CBE](docs/cbe.md) * [CCGA_DX](docs/ccga_dx.md) * [CCGA_MED](docs/ccga_med.md) diff --git a/conf/cambridge.config b/conf/cambridge.config new file mode 100644 index 0000000..3c970b7 --- /dev/null +++ b/conf/cambridge.config @@ -0,0 +1,18 @@ +params { + config_profile_description = 'Cambridge HPC cluster profile.' + config_profile_contact = 'Andries van Tonder (ajv37@cam.ac.uk)' + config_profile_url = "https://docs.hpc.cam.ac.uk/hpc" +} +singularity { + enabled = true + autoMounts = true +} +process { + executor = 'slurm' + clusterOptions = '-p cclake' +} +params { + max_memory = 192.GB + max_cpus = 56 + max_time = 12.h +} diff --git a/docs/cambridge.md b/docs/cambridge.md new file mode 100644 index 0000000..ce833d7 --- /dev/null +++ b/docs/cambridge.md @@ -0,0 +1,18 @@ +# 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.