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Added SHH specific EAGER configuration
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conf/pipeline/eager/shh.config
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conf/pipeline/eager/shh.config
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// Profile config names for nf-core/configs
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params {
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// Specific nf-core/configs params
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config_profile_contact = 'James Fellows Yates (@jfy133)'
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config_profile_description = 'nf-core/eager SHH profile provided by nf-core/configs'
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}
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// Specific nf-core/eager process configuration
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process {
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withName: malt {
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memory = { check_max( 756.GB * task.attempt, 'memory' ) }
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cpus = { check_max(64 * task.attempt, 'cpus') }
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time = 1440.h
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queue = { task.memory > 756.GB ? 'supercruncher': 'long' }
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}
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}
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docs/pipeline/eager/shh.md
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docs/pipeline/eager/shh.md
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# nf-core/configs: shh eager specific configuration
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Extra specific configuration for eager pipeline
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## Usage
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To use, run the pipeline with `-profile shh`.
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This will download and launch the eager specific [`shh.config`](../conf/pipeline/eager/shh.config) which has been pre-configured with a setup suitable for the shh cluster.
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Example: `nextflow run nf-core/eager -profile shh`
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## eager specific configurations for shh
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Specific configurations for shh has been made for eager.
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* Running with the MALT module turned on, will by default be sent either to long or supercruncher queues with a minimum of 756GB and 64 cores.
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pipeline/eager.config
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pipeline/eager.config
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/*
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* -------------------------------------------------
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* nfcore/eager custom profile Nextflow config file
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* -------------------------------------------------
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* Config options for custom environments.
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* Cluster-specific config options should be saved
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* in the conf/pipeline/eager folder and imported
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* under a profile name here.
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*/
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profiles {
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shh { includeConfig "${params.custom_config_base}/conf/pipeline/eager/shh.config" }
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}
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