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nf-configs/conf/pipeline/eager/shh.config

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// Profile config names for nf-core/configs
params {
// Specific nf-core/configs params
config_profile_contact = 'James Fellows Yates (@jfy133)'
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config_profile_description = 'nf-core/eager SHH profile provided by nf-core/configs'
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igenomes_base = "/projects1/public_data/igenomes/"
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// default BWA
bwaalnn = 0.04
bwaalnl = 32
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}
// Specific nf-core/eager process configuration
process {
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withName: malt {
maxRetries = 1
memory = { task.attempt > 1 ? 1900.GB : 725.GB }
cpus = { task.attempt > 1 ? 112 : 64 }
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time = 1440.h
queue = { task.memory > 756.GB ? 'supercruncher' : 'long' }
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}
}
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profiles {
pathogen_loose {
params {
config_profile_description = 'Pathogen (loose) MPI-SHH profile, provided by nf-core/configs.'
bwaalnn = 0.01
bwaalnl = 16
}
}
pathogen_strict {
params {
config_profile_description = 'Pathogen (strict) MPI-SHH SDAG profile, provided by nf-core/configs.'
bwaalnn = 0.1
bwaalnl = 32
}
}
human {
params {
config_profile_description = 'Human MPI-SHH SDAG profile, provided by nf-core/configs.'
bwaalnn = 0.01
bwaalnl = 16500
}
}
}