Build branch main with version main (65dd41d)

Build pipeline: viash-hub.htrnaseq.main-vhms8

Source commit: 65dd41d8b1

Source message: Optimize spawning of processes

target/executable/parallel_map/nextflow_labels.config

@@ -1,26 +1,88 @@
+executor {
+  $k8s {
+    submitRateLimit = '10sec'
+    pollInterval = '1 sec'
+  }
+}
+
 process {
-  // Default resources for components that hardly do any processing
-  memory = { 2.GB * task.attempt }
-  cpus = 1
+  container = 'nextflow/bash:latest'
+  
+  // default resources
+  memory = { 8.Gb * task.attempt }
+  cpus = 8
+  maxForks = 36
 
   // Retry for exit codes that have something to do with memory issues
   errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
   maxRetries = 3
-  maxMemory = null
+  maxMemory = 192.GB
 
   // Resource labels
-  withLabel: singlecpu { cpus = 1 }
-  withLabel: lowcpu { cpus = 4 }
-  withLabel: midcpu { cpus = 10 }
-  withLabel: highcpu { cpus = 20 }
+  withLabel: verylowcpu { cpus = 2 }
+  withLabel: lowcpu { cpus = 8 }
+  withLabel: midcpu { cpus = 16 }
+  withLabel: highcpu { cpus = 32 }
   
-  withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
-  withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
-  withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
-  withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
+  withLabel: verylowmem { memory = { get_memory( 4.GB * task.attempt ) } }
+  withLabel: lowmem { memory = { get_memory( 8.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 64.GB * task.attempt ) } }
 
 }
 
+profiles {
+  // detect tempdir
+  tempDir = java.nio.file.Paths.get(
+    System.getenv('NXF_TEMP') ?:
+      System.getenv('VIASH_TEMP') ?: 
+      System.getenv('TEMPDIR') ?: 
+      System.getenv('TMPDIR') ?: 
+      '/tmp'
+  ).toAbsolutePath()
+
+  mount_temp {
+    docker.temp            = tempDir
+    podman.temp            = tempDir
+    charliecloud.temp      = tempDir
+  }
+
+  no_publish {
+    process {
+      withName: '.*' {
+        publishDir = [
+          enabled: false
+        ]
+      }
+    }
+  }
+
+  docker {
+    docker.fixOwnership    = true
+    docker.enabled         = true
+    // docker.userEmulation   = true
+    singularity.enabled    = false
+    podman.enabled         = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+
+  local {
+    // This config is for local processing.
+    process {
+        maxMemory = 25.GB
+        withLabel: verylowcpu { cpus = 2 }
+        withLabel: lowcpu { cpus = 4 }
+        withLabel: midcpu { cpus = 6 }
+        withLabel: highcpu { cpus = 12 }
+  
+        withLabel: lowmem { memory = { get_memory( 8.GB * task.attempt ) } }
+        withLabel: midmem { memory = { get_memory( 12.GB * task.attempt ) } }
+        withLabel: highmem { memory = { get_memory( 20.GB * task.attempt ) } }
+    }
+  }
+}
+
 def get_memory(to_compare) {
     if (!process.containsKey("maxMemory") || !process.maxMemory) {
       return to_compare