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added leicester profile

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Matiss Ozols 2021-10-21 18:32:57 +01:00
parent 5afa43ad15
commit f8b932ae2d
3 changed files with 25 additions and 0 deletions
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conf/leicester.conf Normal file
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//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'}
}

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docs/leicester.md Normal file
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# 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.

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nfcore_custom.config
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@ -19,6 +19,7 @@ profiles {
binac { includeConfig "${params.custom_config_base}/conf/binac.config" } binac { includeConfig "${params.custom_config_base}/conf/binac.config" }
biohpc_gen { includeConfig "${params.custom_config_base}/conf/biohpc_gen.config" } biohpc_gen { includeConfig "${params.custom_config_base}/conf/biohpc_gen.config" }
cambridge { includeConfig "${params.custom_config_base}/conf/cambridge.config" } cambridge { includeConfig "${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" } cbe { includeConfig "${params.custom_config_base}/conf/cbe.config" }
ccga_dx { includeConfig "${params.custom_config_base}/conf/ccga_dx.config" } ccga_dx { includeConfig "${params.custom_config_base}/conf/ccga_dx.config" }
ccga_med { includeConfig "${params.custom_config_base}/conf/ccga_med.config" } ccga_med { includeConfig "${params.custom_config_base}/conf/ccga_med.config" }