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nextflow.config
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profiles {
standard {
process {
withName: 'trimReads' {
cpus = 10
memory = 12.GB
}
withName: 'filterTp' {
cpus = 16
memory = 32.GB
}
withName: 'mapReads' {
cpus = 10
memory = 12.GB
}
withName: 'deNovoAssembly' {
cpus = 10
memory = 12.GB
}
withName: 'mergeAssemblyMapping' {
cpus = 10
memory = 12.GB
}
withName: 'remapReads' {
cpus = 1
memory = 1.GB
}
withName: 'generateConsensus' {
cpus = 1
memory = 1.GB
}
withName: 'annotateConsensus' {
cpus = 1
memory = 1.GB
}
}
}
Cloud {
process {
withName: 'trimReads' {
cpus = 8
memory = 16.GB
}
withName: 'filterTp' {
cpus = 32
memory = 64.GB
}
withName: 'mapUnmatchedReads' {
cpus = 64
memory = 128.GB
}
withName: 'moreFiltering' {
cpus = 64
memory = 128.GB
}
withName: 'mapReads' {
cpus = 8
memory = 16.GB
}
withName: 'samToBam' {
cpus = 4
memory = 8.GB
}
withName: 'removeDuplicates' {
cpus = 4
memory = 8.GB
}
withName: 'callVariants' {
cpus = 4
memory = 8.GB
}
withName: 'deNovoAssembly' {
cpus = 8
memory = 16.GB
}
withName: 'mergeAssemblyMapping' {
cpus = 4
memory = 8.GB
}
withName: 'remapReads' {
cpus = 4
memory = 8.GB
}
withName: 'pilonPolishing' {
cpus = 4
memory = 8.GB
}
withName: 'remapPilon' {
cpus = 4
memory = 8.GB
}
withName: 'generateConsensus' {
cpus = 16
memory = 32.GB
}
withName: 'generatePilonConsensus' {
cpus = 16
memory = 32.GB
}
withName: 'annotateConsensus' {
cpus = 8
memory = 16.GB
}
withName: 'annotatePilonConsensus' {
cpus = 8
memory = 16.GB
}
}
aws.client.maxParallelTransfers = 2
}
}