memory test

conf/nuig.conf

@@ -1,7 +1,7 @@
 //Profile config names for nf-core/configs
 
 params {
-  config_profile_description = 'National University of Ireland, Galway SLURM cluster profile provided by nf-core/configs'
+  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/nuig.md'
 }
@@ -9,22 +9,24 @@ params {
 singularity {
   enabled = true
   autoMounts = true
-  cacheDir = '/data/bdigby/containers'
+  cacheDir = '/data/containers'
 }
 
 process {
-  beforeScript = 'module load singularity/3.4.1'
+  beforeScript = """
+                    module load EasyBuild/3.4.1
+                    module load Java/1.8.0_144
+                    module load singularity/3.4.1
+                 """
+                 .stripIndent()
   containerOptions = '-B /data/'
   executor = 'slurm'
   queue = { task.cpus > 8 ? 'highmem' : 'normal' }
+  withName: '*' { memory = null }
 }
 
-/*
-  NUIG SLURM is not configured to use the memory parameter, please do not include
-  However, the highmem queue has 128GB memory and the normal queue has 64GB.
-*/
-
 params {
   max_time = '120.d'
+  max_memory = '64.GB'
   max_cpus = '16'
 }

docs/nuig.md

@@ -0,0 +1,15 @@
+# nf-core/configs: National University of Ireland, Galway (Lugh) Configuration
+
+All nf-core pipelines have been successfully configured for use on Lugh at the [National University of Ireland, Galway](http://maths.nuigalway.ie/biocluster/).
+
+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.
+
+## Running nextflow on Lugh
+
+Before running a pipeline you will need a working version of nextflow. Please follow the install instructions below:
+
+- Install Nextflow : [here](https://www.nextflow.io/docs/latest/getstarted.html#)
+
+* 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. 
+
+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.