Merge pull request #161 from ewels/uct_hpc

Update UCT hex -> hpc

.github/workflows/main.yml

@@ -16,7 +16,7 @@ jobs:
     needs: test_all_profiles
     strategy:
         matrix:
-          profile: ['awsbatch', 'bi','bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax', 'utd_ganymede', 'uzh']
+          profile: ['awsbatch', 'bi','bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh']
     steps:
       - uses: actions/checkout@v1
       - name: Install Nextflow
@@ -24,7 +24,7 @@ jobs:
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
       - name: Check ${{ matrix.profile }} profile
-        env: 
+        env:
           SCRATCH: '~'
           NXF_GLOBAL_CONFIG: awsbatch.config
         run: nextflow run ${GITHUB_WORKSPACE}/configtest.nf --custom_config_base=${GITHUB_WORKSPACE} -profile ${{ matrix.profile }}

README.md

@@ -117,7 +117,7 @@ Currently documentation is available for the following systems:
 * [PHOENIX](docs/phoenix.md)
 * [PRINCE](docs/prince.md)
 * [SHH](docs/shh.md)
-* [UCT_HEX](docs/uct_hex.md)
+* [UCT_HPC](docs/uct_hpc.md)
 * [UPPMAX](docs/uppmax.md)
 * [UTD_GANYMEDE](docs/utd_ganymede.md)
 * [UZH](docs/uzh.md)

conf/uct_hex.config

@@ -1,23 +0,0 @@
-//Profile config names for nf-core/configs
-params {
-  config_profile_description = 'University of Cape Town HEX cluster config file provided by nf-core/configs.'
-  config_profile_contact = 'Katie Lennard (@kviljoen)'
-  config_profile_url = 'http://hpc.uct.ac.za/index.php/hex-3/'
-}
-
-singularity {
-   enabled = true
-   cacheDir = "/scratch/DB/bio/singularity-containers"
-}
-
-process {
-   stageInMode = 'symlink'
-   stageOutMode = 'rsync'
-   queue = 'UCTlong'
-   clusterOptions = { "-M $params.email -m abe -l nodes=1:ppn=1:series600" }
-}
-
-executor{
-   executor = 'pbs'
-   jobName = { "$task.tag" }
-}

conf/uct_hpc.config

@@ -0,0 +1,41 @@
+/*
+ * -------------------------------------------------
+ *  HPC cluster config file
+ * -------------------------------------------------
+ * http://www.hpc.uct.ac.za/
+ */
+
+params {
+   config_profile_description = 'University of Cape Town High Performance Cluster config file provided by nf-core/configs.'
+   config_profile_contact = 'Katie Lennard (@kviljoen)'
+   config_profile_url = 'http://hpc.uct.ac.za/index.php/hpc-cluster/'
+
+   singularity_cache_dir = "/bb/DB/bio/singularity-containers/"
+   igenomes_base = '/bb/DB/bio/rna-seq/references'
+   max_memory = 384.GB
+   max_cpus = 40
+   max_time = 1000.h
+   hpc_queue = 'ada'
+   hpc_account = '--account cbio'
+   genome = 'GRCh37'
+}
+
+singularity {
+   enabled = true
+   cacheDir = params.singularity_cache_dir
+   autoMounts = true
+}
+
+process {
+   executor = 'slurm'
+   queue = params.hpc_queue
+   // Increasing maxRetries, this will overwrite what we have in base.config
+   maxRetries = 4
+   clusterOptions = params.hpc_account
+   stageInMode = 'symlink'
+   stageOutMode = 'rsync'
+}
+
+executor {
+   queueSize = 15
+}

docs/uct_hpc.md

@@ -0,0 +1,5 @@
+# nf-core/configs: UCT HPC config
+
+University of Cape Town [High Performance Cluster](http://hpc.uct.ac.za/index.php/hpc-cluster/) config.
+
+For help or more information, please contact Katie Lennard (@kviljoen).

nfcore_custom.config

@@ -35,7 +35,7 @@ profiles {
   phoenix      { includeConfig "${params.custom_config_base}/conf/phoenix.config" }
   prince       { includeConfig "${params.custom_config_base}/conf/prince.config" }
   shh          { includeConfig "${params.custom_config_base}/conf/shh.config" }
-  uct_hex      { includeConfig "${params.custom_config_base}/conf/uct_hex.config" }
+  uct_hpc      { includeConfig "${params.custom_config_base}/conf/uct_hpc.config" }
   uppmax       { includeConfig "${params.custom_config_base}/conf/uppmax.config" }
   utd_ganymede { includeConfig "${params.custom_config_base}/conf/utd_ganymede.config" }
   uzh          { includeConfig "${params.custom_config_base}/conf/uzh.config" }