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Merge pull request #145 from bioatlas/master

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Adding UPPMAX specific config for ampliseq
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Maxime Garcia 2020-03-31 15:46:21 +02:00 committed by GitHub
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1
README.md
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@ -165,6 +165,7 @@ Currently documentation is available for the following pipeline within the speci
* ampliseq
* [BINAC](docs/pipeline/ampliseq/binac.md)
* [UPPMAX](docs/pipeline/ampliseq/uppmax.md)
* eager
* [SHH](docs/pipeline/eager/shh.md)
* rnafusion

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