millironx/nf-configs
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Fixed typo & added singularity tmpdir

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ameyner2 2021-03-15 15:42:30 +00:00
parent bc961c7990
commit cfe13fe6c1
2 changed files with 26 additions and 20 deletions
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44
conf/eddie.config
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@ -5,39 +5,45 @@ params {
config_profile_url = 'https://www.ed.ac.uk/information-services/research-support/research-computing/ecdf/high-performance-computing' config_profile_url = 'https://www.ed.ac.uk/information-services/research-support/research-computing/ecdf/high-performance-computing'
} }
conda { executor {
createTimeout = '2h' name = "sge"
} queueSize = "100"
singularity {
enabled = true
} }
process { process {
executor = 'sge' clusterOptions = { task.memory ? "-l h_vmem=${task.memory.bytes/task.cpus}" : null }
scratch = true
// memory environment & options penv = { task.cpus > 1 ? "sharedmem" : null }
clusterOptions = {"-l h_vmem=${task.memory.bytes/task.cpus}"}
penv = 'sharedmem'
// common SGE error statuses // common SGE error statuses
errorStrategy = {task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish'} errorStrategy = {task.exitStatus in [143,137,104,134,139,140] ? 'retry' : 'finish'}
maxErrors = '-1' maxErrors = '-1'
maxRetries = 3 maxRetries = 3
// load module script for Anaconda and Singularity beforeScript =
beforeScript = { '. /etc/profile.d/modules.sh; sleep 2; ' } """
module = 'anaconda/5.3.1' '. /etc/profile.d/modules.sh
module = 'singularity/3.5.3' sleep 2
module load 'anaconda/5.3.1'
module load 'roslin/singularity/3.5.3'
export SINGULARITY_TMPDIR="\$TMPDIR"
"""
} }
params { params {
saveReference = true saveReference = true
// iGenomes reference base // iGenomes reference base
igenomes_base = '/exports/igmm/eddie/NextGenResources/igenomes/' igenomes_base = '/exports/igmm/eddie/NextGenResources/igenomes'
max_memory = 384.GB max_memory = 384.GB
max_cpus = 32 max_cpus = 32
max_time = 240.h max_time = 240.h
} }
env {
MALLOC_ARENA_MAX=1
}
singularity {
envWhitelist = "SINGULARITY_TMPDIR"
runOptions = '-p'
}

2
nfcore_custom.config
View file

@ -23,7 +23,7 @@ profiles {
crick { includeConfig "${params.custom_config_base}/conf/crick.config" } crick { includeConfig "${params.custom_config_base}/conf/crick.config" }
czbiohub_aws { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" } czbiohub_aws { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" }
ebc { includeConfig "${params.custom_config_base}/conf/ebc.config" } ebc { includeConfig "${params.custom_config_base}/conf/ebc.config" }
eddie { includeConfig "${params.custom_config_bsae}/conf/eddie.config" } eddie { includeConfig "${params.custom_config_base}/conf/eddie.config" }
icr_davros { includeConfig "${params.custom_config_base}/conf/icr_davros.config" } icr_davros { includeConfig "${params.custom_config_base}/conf/icr_davros.config" }
imperial { includeConfig "${params.custom_config_base}/conf/imperial.config" } imperial { includeConfig "${params.custom_config_base}/conf/imperial.config" }
imperial_mb { includeConfig "${params.custom_config_base}/conf/imperial_mb.config" } imperial_mb { includeConfig "${params.custom_config_base}/conf/imperial_mb.config" }