From f8b932ae2d5cf97aa2a2a290ec6b1ee1ca45a650 Mon Sep 17 00:00:00 2001 From: Matiss Ozols Date: Thu, 21 Oct 2021 18:32:57 +0100 Subject: [PATCH] added leicester profile --- conf/leicester.conf | 16 ++++++++++++++++ docs/leicester.md | 8 ++++++++ nfcore_custom.config | 1 + 3 files changed, 25 insertions(+) create mode 100644 conf/leicester.conf create mode 100644 docs/leicester.md diff --git a/conf/leicester.conf b/conf/leicester.conf new file mode 100644 index 0000000..d91a006 --- /dev/null +++ b/conf/leicester.conf @@ -0,0 +1,16 @@ +//Profile config names for nf-core/configs +params { + config_profile_description = 'ALICE and SPECTRE cluster profile provided by nf-core/configs.' + config_profile_contact = 'Matiss Ozols - mo246@leichester.ac.uk | mo11@sanger.ac.uk | matiss.ozols@manchester.ac.uk | mo513@cam.ac.uk' +} + +singularity { + enabled = true + envWhitelist = 'TZ' +} + +process { + executor = 'pbs' + queue = { task.time <= 24.h ? 'short' : task.time > 672.h ? 'long' : 'medium'} +} + diff --git a/docs/leicester.md b/docs/leicester.md new file mode 100644 index 0000000..3118022 --- /dev/null +++ b/docs/leicester.md @@ -0,0 +1,8 @@ +# nf-core/configs: Leicester Configuration + +All nf-core pipelines have been successfully configured for use on the ALICE and SPECTRE cluster at the University of Leicester. Read more about lLicester HPC - https://uniofleicester.sharepoint.com/sites/research-computing/SitePages/alice.aspx + +To use, run the pipeline with `-profile leicester`. This will download and launch the [`leicester.config`](../conf/leicester.config) which has been pre-configured with a setup suitable for the Leicester cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline. + +>NB: You will need an account to use the ALICE and SPECTRE cluster 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. \ No newline at end of file diff --git a/nfcore_custom.config b/nfcore_custom.config index eb5b509..caf1679 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -19,6 +19,7 @@ profiles { binac { includeConfig "${params.custom_config_base}/conf/binac.config" } biohpc_gen { includeConfig "${params.custom_config_base}/conf/biohpc_gen.config" } cambridge { includeConfig "${params.custom_config_base}/conf/cambridge.config" } + leicester { includeConfig "${params.custom_config_base}/conf/leicester.config" } cbe { includeConfig "${params.custom_config_base}/conf/cbe.config" } ccga_dx { includeConfig "${params.custom_config_base}/conf/ccga_dx.config" } ccga_med { includeConfig "${params.custom_config_base}/conf/ccga_med.config" }