nuig.config first commit

.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', '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', 'mpcdf', 'munin', 'nuig', 'oist', 'pasteur', 'phoenix', 'prince', 'sanger', 'seg_globe', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh']
     steps:
       - uses: actions/checkout@v1
       - name: Install Nextflow

README.md

@@ -120,6 +120,7 @@ Currently documentation is available for the following systems:
 * [KRAKEN](docs/kraken.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/nuig.conf

@@ -0,0 +1,30 @@
+//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_contact = 'Barry Digby (@BarryDigby)'
+  config_profile_url = 'https://github.com/nf-core/configs/blob/master/docs/nuig.md'
+}
+
+singularity {
+  enabled = true
+  autoMounts = true
+  cacheDir = '/data/containers'
+}
+
+process {
+  beforeScript = 'module load singularity/3.4.1'
+  containerOptions = '-B /data/'
+  executor = 'slurm'
+  queue = { task.cpus > 8 ? 'highmem' : 'normal' }
+}
+
+/*
+  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_cpus = '16'
+}

nfcore_custom.config

@@ -29,7 +29,7 @@ profiles {
   icr_davros   { includeConfig "${params.custom_config_base}/conf/icr_davros.config" }
   ifb_core     { includeConfig "${params.custom_config_base}/conf/ifb_core.config" }
   imperial     { includeConfig "${params.custom_config_base}/conf/imperial.config" }
-  imperial_mb  { includeConfig "${params.custom_config_base}/conf/imperial_mb.config" }  
+  imperial_mb  { includeConfig "${params.custom_config_base}/conf/imperial_mb.config" }
   genotoul     { includeConfig "${params.custom_config_base}/conf/genotoul.config" }
   google       { includeConfig "${params.custom_config_base}/conf/google.config" }
   denbi_qbic   { includeConfig "${params.custom_config_base}/conf/denbi_qbic.config" }
@@ -39,6 +39,7 @@ profiles {
   kraken       { includeConfig "${params.custom_config_base}/conf/kraken.config" }
   mpcdf        { includeConfig "${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" }