nuig confg (lugh)

.github/workflows/main.yml

@@ -16,7 +16,7 @@ jobs:
     needs: test_all_profiles
     strategy:
         matrix:
-          profile: ['abims', 'awsbatch', 'bi','bigpurple', 'binac', 'biohpc_gen', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'eddie', 'eva', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'ifb_core', 'imperial', 'imperial_mb', 'jax', 'kraken', 'mpcdf', 'munin', 'nuig', 'oist', 'pasteur', 'phoenix', 'prince', 'sanger', 'seg_globe', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh']
+          profile: ['abims', 'awsbatch', 'bi','bigpurple', 'binac', 'biohpc_gen', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'eddie', 'eva', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'ifb_core', 'imperial', 'imperial_mb', 'jax', 'kraken', 'lugh', 'mpcdf', 'munin', 'oist', 'pasteur', 'phoenix', 'prince', 'sanger', 'seg_globe', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh']
     steps:
       - uses: actions/checkout@v1
       - name: Install Nextflow

README.md

@@ -118,9 +118,9 @@ Currently documentation is available for the following systems:
 * [ICR_DAVROS](docs/icr_davros.md)
 * [JAX](docs/jax.md)
 * [KRAKEN](docs/kraken.md)
+* [LUGH](docs/lugh.md)
 * [MPCDF](docs/mpcdf.md)
 * [MUNIN](docs/munin.md)
-* [NUIG](docs/nuig.md)
 * [OIST](docs/oist.md)
 * [PASTEUR](docs/pasteur.md)
 * [PHOENIX](docs/phoenix.md)

conf/lugh.config

@@ -3,7 +3,7 @@
 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/nuig.md'
+  config_profile_url = 'https://github.com/nf-core/configs/blob/master/docs/lugh.md'
 }
 
 singularity {
@@ -17,12 +17,12 @@ process {
                     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.cpus > 8 ? 'highmem' : 'normal' }
-  withName: '*' { memory = null }
+  queue = { task.memory >= 64.GB || task.cpus > 16 ? 'highmem' : 'normal' }
 }
 
 params {

docs/lugh.md

@@ -0,0 +1,18 @@
+# nf-core/configs: LUGH configuration
+
+To use the lugh configuration profile with your pipeline, add `-profile lugh` to your `nextflow run` command. Please take care to use the `-bg` flag or run the job on a compute node. DO NOT RUN ANALYSES ON THE HEAD NODE.
+
+The configuration file will load prerequisite modules for users, however it is entirely up to the user to have a functional version of nextflow installed in their path.
+
+Lugh has 3 queues:
+
+    * `MSC`: compute0{1..3}, 16 cpus, 32GB memory (Please reserve for MSc students only)
+    * `normal`: compute{10..29}, 16 cpus, 64GB memory.
+    & `highmem`: compute0{4..9}, 32 cpus, 128GB memory.
+
+The configuration profile design is very simple. If your process exceeds 64GB memory or 16 cpus, it is sent to the `highmem` queue. Else, `normal`.
+
+Whilst I (@BarryDigby) am happy to help people set up their nextflow pipelines, please note that I am not the system administrator.
+
+### Container Cache
+Your workflow containers will be downloaded and stored at `/data/containers` which is accessible to all users. 

docs/nuig.md

@@ -1,15 +0,0 @@
-# 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.

nfcore_custom.config

@@ -37,9 +37,9 @@ profiles {
   gis          { includeConfig "${params.custom_config_base}/conf/gis.config" }
   hebbe        { includeConfig "${params.custom_config_base}/conf/hebbe.config" }
   kraken       { includeConfig "${params.custom_config_base}/conf/kraken.config" }
+  lugh         { includeConfig "${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" }
-  nuig         { includeConfig "${params.custom_config_base}/conf/nuig.config" }
   oist         { includeConfig "${params.custom_config_base}/conf/oist.config" }
   pasteur      { includeConfig "${params.custom_config_base}/conf/pasteur.config" }
   phoenix      { includeConfig "${params.custom_config_base}/conf/phoenix.config" }