Build branch update_craftbox with version update_craftbox (1c55b60)

Build pipeline: viash-hub.htrnaseq.update-craftbox-wm7mk Source commit: 1c55b60560 Source message: Bump craftbox to v0.3.0
2025-08-28 15:02:08 +00:00
commit b1f45f4bb8
298 changed files with 136518 additions and 0 deletions
--- a/target/executable/parallel_map/nextflow_labels.config
+++ b/target/executable/parallel_map/nextflow_labels.config
@@ -0,0 +1,108 @@
+executor {
+  $k8s {
+    submitRateLimit = '10sec'
+    pollInterval = '1 sec'
+  }
+}
+
+process {
+  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 = 192.GB
+
+  // Resource labels
+  withLabel: verylowcpu { cpus = 2 }
+  withLabel: lowcpu { cpus = 8 }
+  withLabel: midcpu { cpus = 16 }
+  withLabel: highcpu { cpus = 32 }
+  
+  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 {
+        withName: ".*parallel_map_process" {
+          maxForks = 1
+        }
+        maxMemory = 25.GB
+        withLabel: verylowcpu { cpus = 2 }
+        withLabel: lowcpu { cpus = 4 }
+        withLabel: midcpu { cpus = 6 }
+        withLabel: highcpu { cpus = 8 }
+  
+        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
+    }
+
+    try {
+      if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
+        return process.maxMemory
+      }
+      else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
+        return max_memory as nextflow.util.MemoryUnit
+      }
+      else {
+        return to_compare
+      }  
+    } catch (all) {
+          println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
+          System.exit(1)
+    }
+  }