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Merge pull request #204 from jfy133/master

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Add a 'big_data' profile for eager @ SHH
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James A. Fellows Yates 2021-02-04 15:07:52 +01:00 committed by GitHub
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76
conf/pipeline/eager/shh.config
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@ -65,6 +65,82 @@ process {
} }
profiles { profiles {
big_data {
params {
// Specific nf-core/configs params
config_profile_contact = 'James Fellows Yates (@jfy133)'
config_profile_description = 'nf-core/eager big-data SHH profile provided by nf-core/configs'
}
executor {
queueSize = 6
}
process {
maxRetries = 2
withName:malt {
maxRetries = 1
memory = { task.attempt > 1 ? 1900.GB : 725.GB }
cpus = { task.attempt > 1 ? 112 : 64 }
time = 1440.h
queue = { task.memory > 756.GB ? 'supercruncher' : 'long' }
}
withName:hostremoval_input_fastq {
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 32.GB * task.attempt, 'memory' ) }
time = 1440.h
queue = 'long'
}
withLabel:'sc_tiny'{
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 2.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
}
withLabel:'sc_small'{
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
}
withLabel:'sc_medium'{
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
}
withLabel:'mc_small'{
cpus = { check_max( 2, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
}
withLabel:'mc_medium' {
cpus = { check_max( 4, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
}
withLabel:'mc_large'{
cpus = { check_max( 8, 'cpus' ) }
memory = { check_max( 32.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
}
withLabel:'mc_huge'{
cpus = { check_max( 32, 'cpus' ) }
memory = { check_max( 512.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
}
}
}
microbiome_screening { microbiome_screening {
process { process {
// Assuming NCBI NT-sized DB // Assuming NCBI NT-sized DB