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