Merge pull request #262 from BarryDigby/master

NUIG config

.github/workflows/main.yml

@@ -16,7 +16,7 @@ jobs:
     needs: test_all_profiles
     strategy:
         matrix:
-          profile: 
+          profile:
             - 'abims'
             - 'aws_tower'
             - 'awsbatch'
@@ -45,6 +45,7 @@ jobs:
             - 'imperial'
             - 'imperial_mb'
             - 'jax'
+            - 'lugh'
             - 'mpcdf'
             - 'munin'
             - 'oist'

README.md

@@ -118,6 +118,7 @@ Currently documentation is available for the following systems:
 * [HEBBE](docs/hebbe.md)
 * [ICR_DAVROS](docs/icr_davros.md)
 * [JAX](docs/jax.md)
+* [LUGH](docs/lugh.md)
 * [MPCDF](docs/mpcdf.md)
 * [MUNIN](docs/munin.md)
 * [OIST](docs/oist.md)

conf/lugh.config

@@ -0,0 +1,32 @@
+//Profile config names for nf-core/configs
+
+params {
+  config_profile_description = 'National University of Ireland, Galway Lugh cluster profile provided by nf-core/configs'
+  config_profile_contact = 'Barry Digby (@BarryDigby)'
+  config_profile_url = 'https://github.com/nf-core/configs/blob/master/docs/lugh.md'
+}
+
+singularity {
+  enabled = true
+  autoMounts = true
+  cacheDir = '/data/containers'
+}
+
+process {
+  beforeScript = """
+                    module load EasyBuild/3.4.1
+                    module load Java/1.8.0_144
+                    module load singularity/3.4.1
+                    ulimit -s unlimited
+                 """
+                 .stripIndent()
+  containerOptions = '-B /data/'
+  executor = 'slurm'
+  queue = { task.memory >= 64.GB || task.cpus > 16 ? 'highmem' : 'normal' }
+}
+
+params {
+  max_time = 120.h
+  max_memory = 128.GB
+  max_cpus = 32
+}

docs/lugh.md

@@ -0,0 +1,39 @@
+# nf-core/configs: LUGH configuration
+
+Author: Barry Digby
+
+Contact Info: barry.digby@nuigalway.ie
+
+System Administrator: Chris Duke
+
+## Quick Start
+
+To use the lugh configuration profile with your pipeline, add `-profile lugh` to your `nextflow run` command:
+
+```console
+nextflow -bg run nf-core/rnaseq -profile test,nuig
+```
+
+Please take care to use the `-bg` flag, or run the job on a compute node.
+
+:warning: DO NOT RUN ANALYSES ON THE HEAD NODE :warning:
+
+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).
+
+## Queue Resources
+
+| Queue   | Hostnames      | Max Memory | Max CPUS | Max Time |
+|---------|----------------|------------|----------|----------|
+| MSC     | compute[01-03] | 32GB       | 16       | 336.h    |
+| Normal  | compute[10-29] | 64GB       | 16       | 240.h    |
+| Highmem | compute[04-09] | 128GB      | 32       | 2880.h   |
+
+***
+
+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.
+
+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.
+
+## Container Cache
+
+Your workflow containers are stored under `/data/containers/` which is accessible to all users on lugh.

nfcore_custom.config

@@ -39,6 +39,7 @@ profiles {
   imperial     { includeConfig "${params.custom_config_base}/conf/imperial.config" }
   imperial_mb  { includeConfig "${params.custom_config_base}/conf/imperial_mb.config" }  
   jax          { includeConfig "${params.custom_config_base}/conf/jax.config" }
+  lugh         { includeConfig "${params.custom_config_base}/conf/lugh.config" }
   mpcdf        { includeConfig "${params.custom_config_base}/conf/mpcdf.config" }
   munin        { includeConfig "${params.custom_config_base}/conf/munin.config" }
   oist         { includeConfig "${params.custom_config_base}/conf/oist.config" }