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memory test
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//Profile config names for nf-core/configs
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params {
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config_profile_description = 'National University of Ireland, Galway SLURM cluster profile provided by nf-core/configs'
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config_profile_description = 'National University of Ireland, Galway Lugh cluster profile provided by nf-core/configs'
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config_profile_contact = 'Barry Digby (@BarryDigby)'
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config_profile_url = 'https://github.com/nf-core/configs/blob/master/docs/nuig.md'
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}
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singularity {
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enabled = true
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autoMounts = true
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cacheDir = '/data/bdigby/containers'
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cacheDir = '/data/containers'
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}
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process {
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beforeScript = 'module load singularity/3.4.1'
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beforeScript = """
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module load EasyBuild/3.4.1
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module load Java/1.8.0_144
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module load singularity/3.4.1
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"""
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.stripIndent()
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containerOptions = '-B /data/'
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executor = 'slurm'
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queue = { task.cpus > 8 ? 'highmem' : 'normal' }
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withName: '*' { memory = null }
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}
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/*
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NUIG SLURM is not configured to use the memory parameter, please do not include
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However, the highmem queue has 128GB memory and the normal queue has 64GB.
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*/
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params {
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max_time = '120.d'
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max_memory = '64.GB'
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max_cpus = '16'
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}
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15
docs/nuig.md
15
docs/nuig.md
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# nf-core/configs: National University of Ireland, Galway (Lugh) Configuration
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All nf-core pipelines have been successfully configured for use on Lugh at the [National University of Ireland, Galway](http://maths.nuigalway.ie/biocluster/).
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To use, run the pipeline with `-profile nuig`. This will download and launch the [`nuig.config`](../conf/nuig.config) which has been pre-configured with a setup suitable for Lugh. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.
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## Running nextflow on Lugh
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Before running a pipeline you will need a working version of nextflow. Please follow the install instructions below:
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- Install Nextflow : [here](https://www.nextflow.io/docs/latest/getstarted.html#)
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* Install Nextflow edge: download the latest source code from Nextflow GitHub [releases](https://github.com/nextflow-io/nextflow/releases). Unpack source code, compile using `make`, add `nextflow` to your `$PATH` when complete.
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One quirk of Lugh that will produce errors unless addressed: Lugh is not configured to take `memory` parameters in pipelines. This means you will have to make a fork of the pipeline, comment out (`//`) all instances of memory in config files (`nextflow.config`, `base.config`, `test.config` ) AND do away with any instances of `toGiga()` in the pipeline.
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