FIX: strict syntax for alliance_canada

conf/alliance_canada.config

@@ -1,11 +1,30 @@
 params {
-    config_profile_description  = 'Alliance Canada HPC config'
-    config_profile_contact      = 'Jerry Li (@jerryakii)'
+    config_profile_contact      = 'Cian Monnin (github/CMonnin)'
     config_profile_url          = 'https://docs.alliancecan.ca/wiki/Nextflow'
 
+    // default to narval settings if no cluster_name defined
+    cluster_name = System.getenv('CC_CLUSTER') ?: 'narval'
+
+    config_profile_description  = params.cluster_name == 'narval' ? 'Alliance Canada (Narval) cluster profile provided by nf-core/configs.' :
+        params.cluster_name == 'fir' ? 'Alliance Canada (Fir) cluster profile provided by nf-core/configs.' :
+        params.cluster_name == 'nibi' ? 'Alliance Canada (Nibi) cluster profile provided by nf-core/configs.' :
+        params.cluster_name == 'rorqual' ? 'Alliance Canada (Rorqual) cluster profile provided by nf-core/configs.' :
+        params.cluster_name == 'trillium' ? 'Alliance Canada (Trillium) cluster profile provided by nf-core/configs.' :
+        'Alliance Canada HPC config'
+
+    max_cpus                    = params.cluster_name == 'nibi' ? 192 :
+        params.cluster_name == 'rorqual' ? 192 :
+        params.cluster_name == 'fir' ? 192 :
+        params.cluster_name == 'trillium' ? null :
+        64
+    max_memory                  =
+        params.cluster_name == 'narval' ? 249.GB :
+        params.cluster_name == 'nibi' ? 750.GB :
+        params.cluster_name == 'rorqual' ? 750.GB :
+        params.cluster_name == 'fir' ? 750.GB :
+        params.cluster_name == 'trillium' ? null :
+        240.GB
     max_time                    = 168.h
-    max_cpus                    = 64
-    max_memory                  = 240.GB
 }
 
 cleanup = true
@@ -16,109 +35,42 @@ singularity {
 }
 
 apptainer {
-    autoMounts = true }
+    autoMounts = true
+}
 
 // Group name for resource allocation must be supplied as environment variable
 process {
     executor        = 'slurm'
-    clusterOptions  = "--account=${System.getenv('SLURM_ACCOUNT')}"
+    clusterOptions  = params.cluster_name == 'trillium' ? "--account=${System.getenv('SLURM_ACCOUNT')} --nodes=1": "--account=${System.getenv('SLURM_ACCOUNT')}"
     maxRetries      = 1
     errorStrategy   = { task.exitStatus in [125,139] ? 'retry' : 'finish' }
-    cpu             = 1
-    time            = '3h'
+    cpus            = 1
+    time            = '1h'
+
+// NOTE:
+// these resourceLimits are set to baseline CPU for each cluser
+// Currently missing are configs for GPUs
+
     resourceLimits = [
-            memory: 240.GB,
-            cpus: 64,
-            time: 168.h
-        ]
+        cpus: params.cluster_name == 'nibi'? 192 :
+            params.cluster_name == 'rorqual' ? 192 :
+            params.cluster_name == 'fir' ? 192 :
+            params.cluster_name == 'trillium' ? null:
+            64,
+        memory: params.cluster_name == 'narval' ? 249.GB :
+            params.cluster_name == 'nibi' ? 750.GB :
+            params.cluster_name == 'rorqual' ? 750.GB :
+            params.cluster_name == 'fir' ? 750.GB :
+            params.cluster_name == 'trillium' ? null :
+            240.GB,
+        time: 168.h
+    ]
+
 }
 
 executor {
     pollInterval    = '60 sec'
     submitRateLimit = '60/1min'
-    queueSize       = 100
-}
-
-// Cluster name is available as environment variable
-// If not found, default to narval as it has the lowest limits
-hostname = "narval"
-try {
-    hostname = "${System.getenv('HOSTNAME')}"
-} catch (java.io.IOException e) {
-    System.err.println("WARNING: Could not determine current cluster, defaulting to narval")
+    queueSize       = params.cluster_name == 'trillium' ? 500 : 100
 }
 
-// Cluster Narval
-if (hostname.startsWith("narval")) {
-    params.config_profile_description = 'Alliance Canada (Narval) cluster profile provided by nf-core/configs.'
-    params.max_memory = 249.GB
-    params.max_cpus   = 64
-    process {
-        resourceLimits = [
-            memory: 249.GB,
-            cpus: 64,
-            time: 168.h
-        ]
-    }
-}
-
-// Cluster Rorqual
-if (hostname.startsWith("rorqual")) {
-    params.config_profile_description = 'Alliance Canada (Rorqual) cluster profile provided by nf-core/configs.'
-    params.max_memory = 750.GB
-    params.max_cpus   = 192
-    process {
-        resourceLimits = [
-            memory: 750.GB,
-            cpus: 192,
-            time: 168.h
-        ]
-    }
-}
-
-// Cluster Trillium
-if (hostname.startsWith("tri")) {
-    params.config_profile_description = 'Alliance Canada (Trillium) cluster profile provided by nf-core/configs.'
-    params.max_memory = null
-    params.max_cpus   = null
-    process {
-        clusterOptions = "--account=${System.getenv('SLURM_ACCOUNT')} --nodes=1"
-        resourceLimits = [
-            time: 168.h
-        ]
-    }
-    executor {
-        queueSize = 500
-    }
-}
-
-// Cluster Nibi
-if (hostname.contains("nibi")) {
-    params.config_profile_description = 'Alliance Canada (Nibi) cluster profile provided by nf-core/configs.'
-    params.max_memory = 750.GB
-    params.max_cpus   = 192
-    process {
-        resourceLimits = [
-            memory: 750.GB,
-            cpus: 192,
-            time: 168.h
-        ]
-    }
-}
-
-// Cluster Fir
-// not sure what the hostname is so set it as a profile
-profiles {
-    fir {
-        params.config_profile_description = 'Alliance Canada (Fir) cluster profile provided by nf-core/configs.'
-        params.max_memory = 750.GB
-        params.max_cpus   = 192
-        process {
-            resourceLimits = [
-                memory: 750.GB,
-                cpus: 192,
-                time: 168.h
-            ]
-        }
-    }
-}