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Custom config for nf-core eager on Crick's data and cluster

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alexandregilardet 2022-03-15 14:13:58 +00:00 committed by GitHub
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/*
* -------------------------------------------------
* Nextflow custom config file for running nf-core eager on data generated at the Francis Crick Institute
* contact: Alexandre Gilardet alexandre.gilardet@crick.ac.uk
* -------------------------------------------------
* nextflow run nf-core/eager -profile <profile>,crick -c custom.config
* (where <profile> is screening or production for low or high-coverage data
* respectively, or external for very high coverage)
*/
profiles {
screening {
process {
withName:bwa {
cpus = 12
memory = '15 GB'
time = '6h'
}
}
}
production {
process {
withName:adapter_removal {
time = '3d'
}
withName:fastp {
time = '8h'
}
withName:bwa {
cpus = 8
memory = '56 GB'
time = '3d'
}
withName:samtools_filter {
time = '3d'
}
withName:dedup {
cpus = 6
memory = '20 GB'
time = '3d'
}
withName:damageprofiler {
memory = '64 GB'
time = '3d'
errorStrategy = { task.exitStatus in [1,143,137,104,134,139] ? 'retry' : 'finish' }
}
}
}
external {
process {
withName:samtools_filter {
cpus = 12
memory = '72 GB'
}
}
}
}