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Modified uppmax and ampliseq specific config to fit with the divided preparation of the database

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Emelie Nilsso 2020-11-23 21:20:36 +01:00
parent 3cc3445549
commit 2ea06ffab8
1 changed files with 18 additions and 6 deletions
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24
conf/pipeline/ampliseq/uppmax.config
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@ -1,15 +1,27 @@
// Profile config names for nf-core/configs // Profile config names for nf-core/configs
System.err.println("reading from the extra uppmax config, e.g. Daniels")
params { params {
// Specific nf-core/configs params // Specific nf-core/configs params
config_profile_contact = 'Daniel Lundin (daniel.lundin@lnu.se)' config_profile_contact = 'Daniel Lundin (daniel.lundin@lnu.se)'
config_profile_description = 'nf-core/ampliseq UPPMAX profile provided by nf-core/configs' config_profile_description = 'nf-core/ampliseq UPPMAX profile provided by nf-core/configs'
} }
withName: make_SILVA_132_16S_classifier { process {
clusterOptions = { "-A $params.project -C fat -p node -N 1 ${params.clusterOptions ?: ''}" } //"make_classifier" is the older version (just one step) of preparing the database for classification
} withName: make_classifier {
clusterOptions = { "-A $params.project -C fat -p node -N 1 -t 7-00:00:00 ${params.clusterOptions ?: ''}" }
}
withName: classifier { //"clfr_extract_seq" and "clfr_train" is the newer version, where database preparation is split in two to optimise resources
clusterOptions = { "-A $params.project -C fat -p node -N 1 ${params.clusterOptions ?: ''}" } withName: clfr_extract_seq {
clusterOptions = { "-A $params.project -p core -n 1 -t 7-00:00:00 ${params.clusterOptions ?: ''}" }
}
withName: clfr_train {
clusterOptions = { "-A $params.project -C fat -p node -N 1 -t 24:00:00 ${params.clusterOptions ?: ''}" }
}
withName: classifier {
clusterOptions = { "-A $params.project -C fat -p node -N 1 ${params.clusterOptions ?: ''}" }
}
} }