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40 lines
1.7 KiB
Markdown
40 lines
1.7 KiB
Markdown
# nf-core/configs: LUGH configuration
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Author: Barry Digby
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Contact Info: barry.digby@nuigalway.ie
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System Administrator: Chris Duke
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## Quick Start
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To use the lugh configuration profile with your pipeline, add `-profile lugh` to your `nextflow run` command:
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```console
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nextflow -bg run nf-core/rnaseq -profile test,nuig
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```
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Please take care to use the `-bg` flag, or run the job on a compute node.
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:warning: DO NOT RUN ANALYSES ON THE HEAD NODE :warning:
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The configuration file will load prerequisite modules for users (`Java` & `Singularity`), however it is up to the user to have a functional version of `nextflow` installed in their path. Follow `nextflow` installation instructions at the following [link](https://www.nextflow.io/docs/latest/getstarted.html#installation).
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## Queue Resources
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| Queue | Hostnames | Max Memory | Max CPUS | Max Time |
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| ------- | -------------- | ---------- | -------- | -------- |
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| MSC | compute[01-03] | 32GB | 16 | 336.h |
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| Normal | compute[10-29] | 64GB | 16 | 240.h |
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| Highmem | compute[04-09] | 128GB | 32 | 2880.h |
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---
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The configuration profile design is very simple. If your process exceeds 64GB memory or 16 cpus, it is sent to the `highmem` queue. If not, it is sent to the `normal` queue. Please do not use the `MSC` queue, this is reserved for Masters students.
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Take others into consideration when deploying your workflow (do not hog the cluster :pig:). If you need to hammer the cluster with a pipeline, please reach out to me and we can tweak the configuration profile to dispatch jobs to only a handful of compute nodes via hostnames.
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## Container Cache
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Your workflow containers are stored under `/data/containers/` which is accessible to all users on lugh.
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