Merge branch 'master' into master

conf/cheaha.config

@@ -19,20 +19,40 @@ singularity {
     runOptions = "--contain --workdir $scratch_dir"
 }
 
+def getQueues = { time, memory ->
+    def queue_list = ["long"]
+
+    if (time <= 2.h) {
+        queue_list.add("express")
+    }
+
+    if (time <= 12.h) {
+        queue_list.add("short")
+    }
+
+    if (time <= 50.h) {
+        queue_list.add("medium")
+    }
+
+    if (memory >= 300.GB) {
+        queue_list.add("largemem-long")
+
+        if (time <= 50.h) {
+            queue_list.add("largemem")
+        }
+    }
+
+    return queue_list.join(",")
+}
+
 process {
     resourceLimits = [
         memory: 750.GB,
         cpus: 128,
         time: 150.h
     ]
     executor = 'slurm'
-    queue = { task.memory <= 50.GB ? (task.time <= 2.h ? 'express' : task.time <= 12.h ? 'short' : task.time <= 50.h ? 'medium' : 'long') : (task.time <= 50.h ? 'largemem' : 'largemem-long')}
     maxRetries = 3
     beforeScript = 'module load Singularity/3.5.2-GCC-5.4.0-2.26'
-}
-
-params {
-    max_memory = 750.GB
-    max_cpus = 128
-    max_time = 150.h
+    queue = { getQueues( task.time, task.memory ) }
 }

conf/pipeline/taxprofiler/hasta.config

@@ -36,4 +36,10 @@ process {
         memory = { 36.GB * task.attempt }
         time   = { 8.h * task.attempt }
     }
+
+    withName: MULTIQC {
+        cpus   = 2
+        memory = { 4.GB * task.attempt }
+        time   = { 4.h * task.attempt }
+    }
 }