Merge pull request #235 from aunderwo/cambridge

Add Cambridge University HPC config

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)

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
+}

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.