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Update medair.config

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- added path to singularity image for Sentieon
- harmonized alignment
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Gwenna Breton 2022-07-07 13:41:42 +02:00 committed by GitHub
parent 746db14d47
commit 4538e8aa36
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1 changed files with 21 additions and 15 deletions
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conf/medair.config
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@ -1,13 +1,13 @@
//Profile config names for nf-core/configs //Profile config names for nf-core/configs
params { params {
config_profile_description = 'Cluster profile for medair (local cluster of Clinical Genomics Gothenburg)' config_profile_description = 'Cluster profile for medair (local cluster of Clinical Genomics Gothenburg)'
config_profile_contact = 'Clinical Genomics, Gothenburg' config_profile_contact = 'Clinical Genomics, Gothenburg'
config_profile_url = 'https://www.scilifelab.se/units/clinical-genomics-goteborg/' config_profile_url = 'https://www.scilifelab.se/units/clinical-genomics-goteborg/'
} }
//Nextflow parameters //Nextflow parameters
singularity { singularity {
enabled = true enabled = true
cacheDir = "/apps/bio/dependencies/nf-core/singularities" cacheDir = "/apps/bio/dependencies/nf-core/singularities"
} }
@ -15,26 +15,32 @@ profiles {
wgs { wgs {
process { process {
queue = 'wgs.q' queue = 'wgs.q'
executor = 'sge' executor = 'sge'
penv = 'mpi' penv = 'mpi'
process.clusterOptions = '-l excl=1' process.clusterOptions = '-l excl=1'
params.max_cpus = 40 params.max_cpus = 40
params.max_time = 48.h params.max_time = 48.h
params.max_memory = 128.GB params.max_memory = 128.GB
} }
} }
production { production {
process { process {
queue = 'production.q' queue = 'production.q'
executor = 'sge' executor = 'sge'
penv = 'mpi' penv = 'mpi'
process.clusterOptions = '-l excl=1' process.clusterOptions = '-l excl=1'
params.max_cpus = 40 params.max_cpus = 40
params.max_time = 480.h params.max_time = 480.h
params.max_memory = 128.GB params.max_memory = 128.GB
} }
} }
} }
//Specific parameter for pipelines that can use Sentieon (e.g. nf-core/sarek, nf-core/raredisease)
process {
withLabel:'sentieon' {
container = "/apps/bio/singularities/sentieon-211204-peta.simg"
}
}