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Adding UPPMAX specific config for ampliseq

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Daniel Lundin 2020-03-31 15:17:24 +02:00
parent 15574ab849
commit c8de9be701
3 changed files with 37 additions and 1 deletions
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15
conf/pipeline/ampliseq/uppmax.config Normal file
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// Profile config names for nf-core/configs
params {
// Specific nf-core/configs params
config_profile_contact = 'Daniel Lundin (daniel.lundin@lnu.se)'
config_profile_description = 'nf-core/ampliseq UPPMAX profile provided by nf-core/configs'
}
withName: make_SILVA_132_16S_classifier {
clusterOptions = { "-A $params.project -C fat -p node -N 1 ${params.clusterOptions ?: ''}" }
}
withName: classifier {
clusterOptions = { "-A $params.project -C fat -p node -N 1 ${params.clusterOptions ?: ''}" }
}

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docs/pipeline/ampliseq/uppmax.md Normal file
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# nf-core/configs: uppmax ampliseq specific configuration
Extra specific configuration for the ampliseq pipeline.
## Usage
To use, run the pipeline with `-profile uppmax`.
This will download and launch the ampliseq specific [`uppmax.config`](../../../conf/pipeline/ampliseq/uppmax.config) which has been pre-configured with a setup suitable for the UPPMAX cluster.
Example: `nextflow run nf-core/ampliseq -profile uppmax`
## ampliseq specific configurations for uppmax
Specific configurations for UPPMAX has been made for ampliseq.
* Makes sure that a fat node is allocated for training and applying a Bayesian classifier.

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pipeline/ampliseq.config
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profiles {
binac { includeConfig "${params.custom_config_base}/conf/pipeline/ampliseq/binac.config" }
}
profiles {
uppmax { includeConfig "${params.custom_config_base}/conf/pipeline/ampliseq/uppmax.config" }
}