Build branch v0.3 with version v0.3.4 (e6f8b20)

Build pipeline: viash-hub.demultiplex.v0.3-ck9ss Source commit: e6f8b20d70 Source message: Bump version to v0.3.4
2024-12-20 12:50:35 +00:00
39 changed files with 1295 additions and 181 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,9 @@
+# demultiplex v0.3.4
+
+## Minor updates
+
+* Resource labels are now automatically included during build (PR #32).
+
 # demultiplex v0.3.3

 ## Breaking change
--- a/_viash.yaml
+++ b/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.3.3
+version: v0.3.4
 description: |
  Demultiplexing pipeline
 license: MIT
@@ -17,3 +17,5 @@ viash_version: 0.9.0
 config_mods: |
  .requirements.commands := ['ps']
  .runners[.type == 'nextflow'].directives.tag := '$id'
+  .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
+  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
--- a/target/executable/io/interop_summary_to_csv/.config.vsh.yaml
+++ b/target/executable/io/interop_summary_to_csv/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "interop_summary_to_csv"
 namespace: "io"
-version: "v0.3.3"
+version: "v0.3.4"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -38,6 +38,9 @@ resources:
 - type: "bash_script"
  path: "script.sh"
  is_executable: true
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
 info: null
 status: "enabled"
 requirements:
@@ -109,6 +112,8 @@ runners:
      cpu200: "cpus = 200"
      cpu500: "cpus = 500"
      cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
  debug: false
  container: "docker"
 engines:
@@ -116,7 +121,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.3"
+  target_tag: "v0.3.4"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -141,12 +146,12 @@ build_info:
  output: "target/executable/io/interop_summary_to_csv"
  executable: "target/executable/io/interop_summary_to_csv/interop_summary_to_csv"
  viash_version: "0.9.0"
-  git_commit: "e297e8ff45464065384476fe521ab2700ec3739c"
-  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.2-4-ge297e8f"
+  git_commit: "e6f8b20d70be8f47907c08cc3c7802920cc0eee4"
+  git_remote: "https://x-access-token:ghs_FhW4M4TmdkVUw8Om3VZ1e7pO685xf7028pZ3@github.com/viash-hub/demultiplex"
+  git_tag: "v0.3.3-3-ge6f8b20"
 package_config:
  name: "demultiplex"
-  version: "v0.3.3"
+  version: "v0.3.4"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -157,10 +162,12 @@ package_config:
  target: "target"
  config_mods:
  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
-    \ := '$id'\n"
+    \ := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n\
+    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
+    )'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.4'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/executable/io/interop_summary_to_csv/interop_summary_to_csv
+++ b/target/executable/io/interop_summary_to_csv/interop_summary_to_csv
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# interop_summary_to_csv v0.3.3
+# interop_summary_to_csv v0.3.4
 # 
 # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "interop_summary_to_csv v0.3.3"
+  echo "interop_summary_to_csv v0.3.4"
  echo ""
  echo "Input arguments:"
  echo "    --input"
@@ -470,10 +470,10 @@ tar -C /tmp/ --no-same-owner --no-same-permissions -xvf /tmp/interop.tar.gz && \
 mv /tmp/interop-1.3.1-Linux-GNU/bin/index-summary /tmp/interop-1.3.1-Linux-GNU/bin/summary /usr/local/bin/

 LABEL org.opencontainers.image.description="Companion container for running component io interop_summary_to_csv"
-LABEL org.opencontainers.image.created="2024-12-19T15:42:23Z"
+LABEL org.opencontainers.image.created="2024-12-20T12:37:34Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="e297e8ff45464065384476fe521ab2700ec3739c"
-LABEL org.opencontainers.image.version="v0.3.3"
+LABEL org.opencontainers.image.revision="e6f8b20d70be8f47907c08cc3c7802920cc0eee4"
+LABEL org.opencontainers.image.version="v0.3.4"

 VIASHDOCKER
  fi
@@ -609,7 +609,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "interop_summary_to_csv v0.3.3"
+            echo "interop_summary_to_csv v0.3.4"
            exit
            ;;
        --input)
@@ -733,7 +733,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/interop_summary_to_csv:v0.3.3'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/interop_summary_to_csv:v0.3.4'
  fi

  # print dockerfile
--- a/target/executable/io/interop_summary_to_csv/nextflow_labels.config
+++ b/target/executable/io/interop_summary_to_csv/nextflow_labels.config
@@ -0,0 +1,98 @@
+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 {
+        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
+    }
+
+    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)
+    }
+  }
--- a/target/executable/io/publish/.config.vsh.yaml
+++ b/target/executable/io/publish/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "publish"
 namespace: "io"
-version: "v0.3.3"
+version: "v0.3.4"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -94,6 +94,9 @@ resources:
 - type: "bash_script"
  path: "code.sh"
  is_executable: true
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
 description: "Publish the processed results of the run"
 info: null
 status: "enabled"
@@ -166,6 +169,8 @@ runners:
      cpu200: "cpus = 200"
      cpu500: "cpus = 500"
      cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
  debug: false
  container: "docker"
 engines:
@@ -173,7 +178,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.3"
+  target_tag: "v0.3.4"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -191,12 +196,12 @@ build_info:
  output: "target/executable/io/publish"
  executable: "target/executable/io/publish/publish"
  viash_version: "0.9.0"
-  git_commit: "e297e8ff45464065384476fe521ab2700ec3739c"
-  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.2-4-ge297e8f"
+  git_commit: "e6f8b20d70be8f47907c08cc3c7802920cc0eee4"
+  git_remote: "https://x-access-token:ghs_FhW4M4TmdkVUw8Om3VZ1e7pO685xf7028pZ3@github.com/viash-hub/demultiplex"
+  git_tag: "v0.3.3-3-ge6f8b20"
 package_config:
  name: "demultiplex"
-  version: "v0.3.3"
+  version: "v0.3.4"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -207,10 +212,12 @@ package_config:
  target: "target"
  config_mods:
  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
-    \ := '$id'\n"
+    \ := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n\
+    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
+    )'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.4'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/executable/io/publish/nextflow_labels.config
+++ b/target/executable/io/publish/nextflow_labels.config
@@ -0,0 +1,98 @@
+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 {
+        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
+    }
+
+    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)
+    }
+  }
--- a/target/executable/io/publish/publish
+++ b/target/executable/io/publish/publish
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# publish v0.3.3
+# publish v0.3.4
 # 
 # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "publish v0.3.3"
+  echo "publish v0.3.4"
  echo ""
  echo "Publish the processed results of the run"
  echo ""
@@ -490,10 +490,10 @@ RUN apt-get update && \
  rm -rf /var/lib/apt/lists/*

 LABEL org.opencontainers.image.description="Companion container for running component io publish"
-LABEL org.opencontainers.image.created="2024-12-19T15:42:24Z"
+LABEL org.opencontainers.image.created="2024-12-20T12:37:34Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="e297e8ff45464065384476fe521ab2700ec3739c"
-LABEL org.opencontainers.image.version="v0.3.3"
+LABEL org.opencontainers.image.revision="e6f8b20d70be8f47907c08cc3c7802920cc0eee4"
+LABEL org.opencontainers.image.version="v0.3.4"

 VIASHDOCKER
  fi
@@ -629,7 +629,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "publish v0.3.3"
+            echo "publish v0.3.4"
            exit
            ;;
        --input)
@@ -808,7 +808,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/publish:v0.3.3'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/publish:v0.3.4'
  fi

  # print dockerfile
--- a/target/executable/io/untar/.config.vsh.yaml
+++ b/target/executable/io/untar/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "untar"
 namespace: "io"
-version: "v0.3.3"
+version: "v0.3.4"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -45,6 +45,9 @@ resources:
 - type: "bash_script"
  path: "script.sh"
  is_executable: true
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
 description: "Unpack a .tar file. When the contents of the .tar file is just a single\
  \ directory,\nput the contents of the directory into the output folder instead of\
  \ that directory.\n"
@@ -123,6 +126,8 @@ runners:
      cpu200: "cpus = 200"
      cpu500: "cpus = 500"
      cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
  debug: false
  container: "docker"
 engines:
@@ -130,7 +135,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.3"
+  target_tag: "v0.3.4"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -148,12 +153,12 @@ build_info:
  output: "target/executable/io/untar"
  executable: "target/executable/io/untar/untar"
  viash_version: "0.9.0"
-  git_commit: "e297e8ff45464065384476fe521ab2700ec3739c"
-  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.2-4-ge297e8f"
+  git_commit: "e6f8b20d70be8f47907c08cc3c7802920cc0eee4"
+  git_remote: "https://x-access-token:ghs_FhW4M4TmdkVUw8Om3VZ1e7pO685xf7028pZ3@github.com/viash-hub/demultiplex"
+  git_tag: "v0.3.3-3-ge6f8b20"
 package_config:
  name: "demultiplex"
-  version: "v0.3.3"
+  version: "v0.3.4"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -164,10 +169,12 @@ package_config:
  target: "target"
  config_mods:
  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
-    \ := '$id'\n"
+    \ := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n\
+    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
+    )'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.4'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/executable/io/untar/nextflow_labels.config
+++ b/target/executable/io/untar/nextflow_labels.config
@@ -0,0 +1,98 @@
+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 {
+        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
+    }
+
+    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)
+    }
+  }
--- a/target/executable/io/untar/untar
+++ b/target/executable/io/untar/untar
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# untar v0.3.3
+# untar v0.3.4
 # 
 # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "untar v0.3.3"
+  echo "untar v0.3.4"
  echo ""
  echo "Unpack a .tar file. When the contents of the .tar file is just a single"
  echo "directory,"
@@ -476,10 +476,10 @@ RUN apt-get update && \
  rm -rf /var/lib/apt/lists/*

 LABEL org.opencontainers.image.description="Companion container for running component io untar"
-LABEL org.opencontainers.image.created="2024-12-19T15:42:24Z"
+LABEL org.opencontainers.image.created="2024-12-20T12:37:34Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="e297e8ff45464065384476fe521ab2700ec3739c"
-LABEL org.opencontainers.image.version="v0.3.3"
+LABEL org.opencontainers.image.revision="e6f8b20d70be8f47907c08cc3c7802920cc0eee4"
+LABEL org.opencontainers.image.version="v0.3.4"

 VIASHDOCKER
  fi
@@ -615,7 +615,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "untar v0.3.3"
+            echo "untar v0.3.4"
            exit
            ;;
        --input)
@@ -745,7 +745,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/untar:v0.3.3'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/untar:v0.3.4'
  fi

  # print dockerfile
--- a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml
+++ b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "combine_samples"
 namespace: "dataflow"
-version: "v0.3.3"
+version: "v0.3.4"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -55,6 +55,9 @@ resources:
  path: "main.nf"
  is_executable: true
  entrypoint: "run_wf"
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
 description: "Combine fastq files from across samples into one event with a list of\
  \ fastq files per orientation."
 info: null
@@ -125,6 +128,8 @@ runners:
      cpu200: "cpus = 200"
      cpu500: "cpus = 500"
      cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
  debug: false
  container: "docker"
 engines:
@@ -139,12 +144,12 @@ build_info:
  output: "target/nextflow/dataflow/combine_samples"
  executable: "target/nextflow/dataflow/combine_samples/main.nf"
  viash_version: "0.9.0"
-  git_commit: "e297e8ff45464065384476fe521ab2700ec3739c"
-  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.2-4-ge297e8f"
+  git_commit: "e6f8b20d70be8f47907c08cc3c7802920cc0eee4"
+  git_remote: "https://x-access-token:ghs_FhW4M4TmdkVUw8Om3VZ1e7pO685xf7028pZ3@github.com/viash-hub/demultiplex"
+  git_tag: "v0.3.3-3-ge6f8b20"
 package_config:
  name: "demultiplex"
-  version: "v0.3.3"
+  version: "v0.3.4"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -155,10 +160,12 @@ package_config:
  target: "target"
  config_mods:
  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
-    \ := '$id'\n"
+    \ := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n\
+    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
+    )'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.4'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/dataflow/combine_samples/main.nf
+++ b/target/nextflow/dataflow/combine_samples/main.nf
@@ -1,4 +1,4 @@
-// combine_samples v0.3.3
+// combine_samples v0.3.4
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2806,7 +2806,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "combine_samples",
  "namespace" : "dataflow",
-  "version" : "v0.3.3",
+  "version" : "v0.3.4",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -2874,6 +2874,11 @@ meta = [
      "path" : "main.nf",
      "is_executable" : true,
      "entrypoint" : "run_wf"
+    },
+    {
+      "type" : "file",
+      "path" : "/src/config/labels.config",
+      "dest" : "nextflow_labels.config"
    }
  ],
  "description" : "Combine fastq files from across samples into one event with a list of fastq files per orientation.",
@@ -2950,7 +2955,10 @@ meta = [
          "cpu200" : "cpus = 200",
          "cpu500" : "cpus = 500",
          "cpu1000" : "cpus = 1000"
-        }
+        },
+        "script" : [
+          "includeConfig(\\"nextflow_labels.config\\")"
+        ]
      },
      "debug" : false,
      "container" : "docker"
@@ -2972,13 +2980,13 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/dataflow/combine_samples",
    "viash_version" : "0.9.0",
-    "git_commit" : "e297e8ff45464065384476fe521ab2700ec3739c",
-    "git_remote" : "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.3.2-4-ge297e8f"
+    "git_commit" : "e6f8b20d70be8f47907c08cc3c7802920cc0eee4",
+    "git_remote" : "https://x-access-token:ghs_FhW4M4TmdkVUw8Om3VZ1e7pO685xf7028pZ3@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.3.3-3-ge6f8b20"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.3.3",
+    "version" : "v0.3.4",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -2992,10 +3000,10 @@ meta = [
    "source" : "src",
    "target" : "target",
    "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
+      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.3'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.4'"
    ],
    "keywords" : [
      "bioinformatics",
--- a/target/nextflow/dataflow/combine_samples/nextflow.config
+++ b/target/nextflow/dataflow/combine_samples/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'dataflow/combine_samples'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.3.3'
+  version = 'v0.3.4'
  description = 'Combine fastq files from across samples into one event with a list of fastq files per orientation.'
 }

@@ -122,4 +122,4 @@ process{
  withLabel: cpu1000 { cpus = 1000 }
 }

-
+includeConfig("nextflow_labels.config")
--- a/target/nextflow/dataflow/combine_samples/nextflow_labels.config
+++ b/target/nextflow/dataflow/combine_samples/nextflow_labels.config
@@ -0,0 +1,98 @@
+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 {
+        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
+    }
+
+    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)
+    }
+  }
--- a/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml
+++ b/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "gather_fastqs_and_validate"
 namespace: "dataflow"
-version: "v0.3.3"
+version: "v0.3.4"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -49,6 +49,9 @@ resources:
  path: "main.nf"
  is_executable: true
  entrypoint: "run_wf"
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
 description: "From a directory containing fastq files, gather the files per sample\
  \ \nand validate according to the contents of the sample sheet.\n"
 info: null
@@ -119,6 +122,8 @@ runners:
      cpu200: "cpus = 200"
      cpu500: "cpus = 500"
      cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
  debug: false
  container: "docker"
 engines:
@@ -133,12 +138,12 @@ build_info:
  output: "target/nextflow/dataflow/gather_fastqs_and_validate"
  executable: "target/nextflow/dataflow/gather_fastqs_and_validate/main.nf"
  viash_version: "0.9.0"
-  git_commit: "e297e8ff45464065384476fe521ab2700ec3739c"
-  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.2-4-ge297e8f"
+  git_commit: "e6f8b20d70be8f47907c08cc3c7802920cc0eee4"
+  git_remote: "https://x-access-token:ghs_FhW4M4TmdkVUw8Om3VZ1e7pO685xf7028pZ3@github.com/viash-hub/demultiplex"
+  git_tag: "v0.3.3-3-ge6f8b20"
 package_config:
  name: "demultiplex"
-  version: "v0.3.3"
+  version: "v0.3.4"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -149,10 +154,12 @@ package_config:
  target: "target"
  config_mods:
  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
-    \ := '$id'\n"
+    \ := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n\
+    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
+    )'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.4'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
+++ b/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
@@ -1,4 +1,4 @@
-// gather_fastqs_and_validate v0.3.3
+// gather_fastqs_and_validate v0.3.4
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2806,7 +2806,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "gather_fastqs_and_validate",
  "namespace" : "dataflow",
-  "version" : "v0.3.3",
+  "version" : "v0.3.4",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -2867,6 +2867,11 @@ meta = [
      "path" : "main.nf",
      "is_executable" : true,
      "entrypoint" : "run_wf"
+    },
+    {
+      "type" : "file",
+      "path" : "/src/config/labels.config",
+      "dest" : "nextflow_labels.config"
    }
  ],
  "description" : "From a directory containing fastq files, gather the files per sample \nand validate according to the contents of the sample sheet.\n",
@@ -2943,7 +2948,10 @@ meta = [
          "cpu200" : "cpus = 200",
          "cpu500" : "cpus = 500",
          "cpu1000" : "cpus = 1000"
-        }
+        },
+        "script" : [
+          "includeConfig(\\"nextflow_labels.config\\")"
+        ]
      },
      "debug" : false,
      "container" : "docker"
@@ -2965,13 +2973,13 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/dataflow/gather_fastqs_and_validate",
    "viash_version" : "0.9.0",
-    "git_commit" : "e297e8ff45464065384476fe521ab2700ec3739c",
-    "git_remote" : "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.3.2-4-ge297e8f"
+    "git_commit" : "e6f8b20d70be8f47907c08cc3c7802920cc0eee4",
+    "git_remote" : "https://x-access-token:ghs_FhW4M4TmdkVUw8Om3VZ1e7pO685xf7028pZ3@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.3.3-3-ge6f8b20"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.3.3",
+    "version" : "v0.3.4",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -2985,10 +2993,10 @@ meta = [
    "source" : "src",
    "target" : "target",
    "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
+      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.3'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.4'"
    ],
    "keywords" : [
      "bioinformatics",
--- a/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow.config
+++ b/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'dataflow/gather_fastqs_and_validate'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.3.3'
+  version = 'v0.3.4'
  description = 'From a directory containing fastq files, gather the files per sample \nand validate according to the contents of the sample sheet.\n'
 }

@@ -122,4 +122,4 @@ process{
  withLabel: cpu1000 { cpus = 1000 }
 }

-
+includeConfig("nextflow_labels.config")
--- a/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow_labels.config
+++ b/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow_labels.config
@@ -0,0 +1,98 @@
+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 {
+        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
+    }
+
+    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)
+    }
+  }
--- a/target/nextflow/demultiplex/.config.vsh.yaml
+++ b/target/nextflow/demultiplex/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "demultiplex"
-version: "v0.3.3"
+version: "v0.3.4"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -101,6 +101,9 @@ resources:
  path: "main.nf"
  is_executable: true
  entrypoint: "run_wf"
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
 description: "Demultiplexing of raw sequencing data"
 test_resources:
 - type: "nextflow_script"
@@ -217,6 +220,8 @@ runners:
      cpu200: "cpus = 200"
      cpu500: "cpus = 500"
      cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
  debug: false
  container: "docker"
 engines:
@@ -231,9 +236,9 @@ build_info:
  output: "target/nextflow/demultiplex"
  executable: "target/nextflow/demultiplex/main.nf"
  viash_version: "0.9.0"
-  git_commit: "e297e8ff45464065384476fe521ab2700ec3739c"
-  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.2-4-ge297e8f"
+  git_commit: "e6f8b20d70be8f47907c08cc3c7802920cc0eee4"
+  git_remote: "https://x-access-token:ghs_FhW4M4TmdkVUw8Om3VZ1e7pO685xf7028pZ3@github.com/viash-hub/demultiplex"
+  git_tag: "v0.3.3-3-ge6f8b20"
  dependencies:
  - "target/nextflow/io/untar"
  - "target/nextflow/dataflow/gather_fastqs_and_validate"
@@ -245,7 +250,7 @@ build_info:
  - "target/dependencies/vsh/vsh/biobox/v0.3.0/nextflow/multiqc"
 package_config:
  name: "demultiplex"
-  version: "v0.3.3"
+  version: "v0.3.4"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -256,10 +261,12 @@ package_config:
  target: "target"
  config_mods:
  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
-    \ := '$id'\n"
+    \ := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n\
+    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
+    )'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.4'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/demultiplex/main.nf
+++ b/target/nextflow/demultiplex/main.nf
@@ -1,4 +1,4 @@
-// demultiplex v0.3.3
+// demultiplex v0.3.4
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2805,7 +2805,7 @@ meta = [
  "resources_dir": moduleDir.toRealPath().normalize(),
  "config": processConfig(readJsonBlob('''{
  "name" : "demultiplex",
-  "version" : "v0.3.3",
+  "version" : "v0.3.4",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -2923,6 +2923,11 @@ meta = [
      "path" : "main.nf",
      "is_executable" : true,
      "entrypoint" : "run_wf"
+    },
+    {
+      "type" : "file",
+      "path" : "/src/config/labels.config",
+      "dest" : "nextflow_labels.config"
    }
  ],
  "description" : "Demultiplexing of raw sequencing data",
@@ -3079,7 +3084,10 @@ meta = [
          "cpu200" : "cpus = 200",
          "cpu500" : "cpus = 500",
          "cpu1000" : "cpus = 1000"
-        }
+        },
+        "script" : [
+          "includeConfig(\\"nextflow_labels.config\\")"
+        ]
      },
      "debug" : false,
      "container" : "docker"
@@ -3101,13 +3109,13 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/demultiplex",
    "viash_version" : "0.9.0",
-    "git_commit" : "e297e8ff45464065384476fe521ab2700ec3739c",
-    "git_remote" : "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.3.2-4-ge297e8f"
+    "git_commit" : "e6f8b20d70be8f47907c08cc3c7802920cc0eee4",
+    "git_remote" : "https://x-access-token:ghs_FhW4M4TmdkVUw8Om3VZ1e7pO685xf7028pZ3@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.3.3-3-ge6f8b20"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.3.3",
+    "version" : "v0.3.4",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -3121,10 +3129,10 @@ meta = [
    "source" : "src",
    "target" : "target",
    "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
+      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.3'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.4'"
    ],
    "keywords" : [
      "bioinformatics",
--- a/target/nextflow/demultiplex/nextflow.config
+++ b/target/nextflow/demultiplex/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'demultiplex'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.3.3'
+  version = 'v0.3.4'
  description = 'Demultiplexing of raw sequencing data'
 }

@@ -122,4 +122,4 @@ process{
  withLabel: cpu1000 { cpus = 1000 }
 }

-
+includeConfig("nextflow_labels.config")
--- a/target/nextflow/demultiplex/nextflow_labels.config
+++ b/target/nextflow/demultiplex/nextflow_labels.config
@@ -0,0 +1,98 @@
+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 {
+        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
+    }
+
+    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)
+    }
+  }
--- a/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml
+++ b/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "interop_summary_to_csv"
 namespace: "io"
-version: "v0.3.3"
+version: "v0.3.4"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -38,6 +38,9 @@ resources:
 - type: "bash_script"
  path: "script.sh"
  is_executable: true
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
 info: null
 status: "enabled"
 requirements:
@@ -109,6 +112,8 @@ runners:
      cpu200: "cpus = 200"
      cpu500: "cpus = 500"
      cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
  debug: false
  container: "docker"
 engines:
@@ -116,7 +121,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.3"
+  target_tag: "v0.3.4"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -141,12 +146,12 @@ build_info:
  output: "target/nextflow/io/interop_summary_to_csv"
  executable: "target/nextflow/io/interop_summary_to_csv/main.nf"
  viash_version: "0.9.0"
-  git_commit: "e297e8ff45464065384476fe521ab2700ec3739c"
-  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.2-4-ge297e8f"
+  git_commit: "e6f8b20d70be8f47907c08cc3c7802920cc0eee4"
+  git_remote: "https://x-access-token:ghs_FhW4M4TmdkVUw8Om3VZ1e7pO685xf7028pZ3@github.com/viash-hub/demultiplex"
+  git_tag: "v0.3.3-3-ge6f8b20"
 package_config:
  name: "demultiplex"
-  version: "v0.3.3"
+  version: "v0.3.4"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -157,10 +162,12 @@ package_config:
  target: "target"
  config_mods:
  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
-    \ := '$id'\n"
+    \ := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n\
+    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
+    )'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.4'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/io/interop_summary_to_csv/main.nf
+++ b/target/nextflow/io/interop_summary_to_csv/main.nf
@@ -1,4 +1,4 @@
-// interop_summary_to_csv v0.3.3
+// interop_summary_to_csv v0.3.4
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2806,7 +2806,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "interop_summary_to_csv",
  "namespace" : "io",
-  "version" : "v0.3.3",
+  "version" : "v0.3.4",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -2855,6 +2855,11 @@ meta = [
      "type" : "bash_script",
      "path" : "script.sh",
      "is_executable" : true
+    },
+    {
+      "type" : "file",
+      "path" : "/src/config/labels.config",
+      "dest" : "nextflow_labels.config"
    }
  ],
  "status" : "enabled",
@@ -2935,7 +2940,10 @@ meta = [
          "cpu200" : "cpus = 200",
          "cpu500" : "cpus = 500",
          "cpu1000" : "cpus = 1000"
-        }
+        },
+        "script" : [
+          "includeConfig(\\"nextflow_labels.config\\")"
+        ]
      },
      "debug" : false,
      "container" : "docker"
@@ -2947,7 +2955,7 @@ meta = [
      "id" : "docker",
      "image" : "debian:stable-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.3.3",
+      "target_tag" : "v0.3.4",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -2977,13 +2985,13 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/interop_summary_to_csv",
    "viash_version" : "0.9.0",
-    "git_commit" : "e297e8ff45464065384476fe521ab2700ec3739c",
-    "git_remote" : "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.3.2-4-ge297e8f"
+    "git_commit" : "e6f8b20d70be8f47907c08cc3c7802920cc0eee4",
+    "git_remote" : "https://x-access-token:ghs_FhW4M4TmdkVUw8Om3VZ1e7pO685xf7028pZ3@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.3.3-3-ge6f8b20"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.3.3",
+    "version" : "v0.3.4",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -2997,10 +3005,10 @@ meta = [
    "source" : "src",
    "target" : "target",
    "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
+      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.3'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.4'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3423,7 +3431,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/demultiplex/io/interop_summary_to_csv",
-    "tag" : "v0.3.3"
+    "tag" : "v0.3.4"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/io/interop_summary_to_csv/nextflow.config
+++ b/target/nextflow/io/interop_summary_to_csv/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'io/interop_summary_to_csv'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.3.3'
+  version = 'v0.3.4'
 }

 process.container = 'nextflow/bash:latest'
@@ -121,4 +121,4 @@ process{
  withLabel: cpu1000 { cpus = 1000 }
 }

-
+includeConfig("nextflow_labels.config")
--- a/target/nextflow/io/interop_summary_to_csv/nextflow_labels.config
+++ b/target/nextflow/io/interop_summary_to_csv/nextflow_labels.config
@@ -0,0 +1,98 @@
+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 {
+        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
+    }
+
+    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)
+    }
+  }
--- a/target/nextflow/io/publish/.config.vsh.yaml
+++ b/target/nextflow/io/publish/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "publish"
 namespace: "io"
-version: "v0.3.3"
+version: "v0.3.4"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -94,6 +94,9 @@ resources:
 - type: "bash_script"
  path: "code.sh"
  is_executable: true
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
 description: "Publish the processed results of the run"
 info: null
 status: "enabled"
@@ -166,6 +169,8 @@ runners:
      cpu200: "cpus = 200"
      cpu500: "cpus = 500"
      cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
  debug: false
  container: "docker"
 engines:
@@ -173,7 +178,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.3"
+  target_tag: "v0.3.4"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -191,12 +196,12 @@ build_info:
  output: "target/nextflow/io/publish"
  executable: "target/nextflow/io/publish/main.nf"
  viash_version: "0.9.0"
-  git_commit: "e297e8ff45464065384476fe521ab2700ec3739c"
-  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.2-4-ge297e8f"
+  git_commit: "e6f8b20d70be8f47907c08cc3c7802920cc0eee4"
+  git_remote: "https://x-access-token:ghs_FhW4M4TmdkVUw8Om3VZ1e7pO685xf7028pZ3@github.com/viash-hub/demultiplex"
+  git_tag: "v0.3.3-3-ge6f8b20"
 package_config:
  name: "demultiplex"
-  version: "v0.3.3"
+  version: "v0.3.4"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -207,10 +212,12 @@ package_config:
  target: "target"
  config_mods:
  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
-    \ := '$id'\n"
+    \ := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n\
+    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
+    )'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.4'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/io/publish/main.nf
+++ b/target/nextflow/io/publish/main.nf
@@ -1,4 +1,4 @@
-// publish v0.3.3
+// publish v0.3.4
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2806,7 +2806,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "publish",
  "namespace" : "io",
-  "version" : "v0.3.3",
+  "version" : "v0.3.4",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -2920,6 +2920,11 @@ meta = [
      "type" : "bash_script",
      "path" : "./code.sh",
      "is_executable" : true
+    },
+    {
+      "type" : "file",
+      "path" : "/src/config/labels.config",
+      "dest" : "nextflow_labels.config"
    }
  ],
  "description" : "Publish the processed results of the run",
@@ -3001,7 +3006,10 @@ meta = [
          "cpu200" : "cpus = 200",
          "cpu500" : "cpus = 500",
          "cpu1000" : "cpus = 1000"
-        }
+        },
+        "script" : [
+          "includeConfig(\\"nextflow_labels.config\\")"
+        ]
      },
      "debug" : false,
      "container" : "docker"
@@ -3013,7 +3021,7 @@ meta = [
      "id" : "docker",
      "image" : "debian:stable-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.3.3",
+      "target_tag" : "v0.3.4",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3036,13 +3044,13 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/publish",
    "viash_version" : "0.9.0",
-    "git_commit" : "e297e8ff45464065384476fe521ab2700ec3739c",
-    "git_remote" : "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.3.2-4-ge297e8f"
+    "git_commit" : "e6f8b20d70be8f47907c08cc3c7802920cc0eee4",
+    "git_remote" : "https://x-access-token:ghs_FhW4M4TmdkVUw8Om3VZ1e7pO685xf7028pZ3@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.3.3-3-ge6f8b20"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.3.3",
+    "version" : "v0.3.4",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -3056,10 +3064,10 @@ meta = [
    "source" : "src",
    "target" : "target",
    "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
+      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.3'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.4'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3503,7 +3511,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/demultiplex/io/publish",
-    "tag" : "v0.3.3"
+    "tag" : "v0.3.4"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/io/publish/nextflow.config
+++ b/target/nextflow/io/publish/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'io/publish'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.3.3'
+  version = 'v0.3.4'
  description = 'Publish the processed results of the run'
 }

@@ -122,4 +122,4 @@ process{
  withLabel: cpu1000 { cpus = 1000 }
 }

-
+includeConfig("nextflow_labels.config")
--- a/target/nextflow/io/publish/nextflow_labels.config
+++ b/target/nextflow/io/publish/nextflow_labels.config
@@ -0,0 +1,98 @@
+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 {
+        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
+    }
+
+    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)
+    }
+  }
--- a/target/nextflow/io/untar/.config.vsh.yaml
+++ b/target/nextflow/io/untar/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "untar"
 namespace: "io"
-version: "v0.3.3"
+version: "v0.3.4"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -45,6 +45,9 @@ resources:
 - type: "bash_script"
  path: "script.sh"
  is_executable: true
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
 description: "Unpack a .tar file. When the contents of the .tar file is just a single\
  \ directory,\nput the contents of the directory into the output folder instead of\
  \ that directory.\n"
@@ -123,6 +126,8 @@ runners:
      cpu200: "cpus = 200"
      cpu500: "cpus = 500"
      cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
  debug: false
  container: "docker"
 engines:
@@ -130,7 +135,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.3"
+  target_tag: "v0.3.4"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -148,12 +153,12 @@ build_info:
  output: "target/nextflow/io/untar"
  executable: "target/nextflow/io/untar/main.nf"
  viash_version: "0.9.0"
-  git_commit: "e297e8ff45464065384476fe521ab2700ec3739c"
-  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.2-4-ge297e8f"
+  git_commit: "e6f8b20d70be8f47907c08cc3c7802920cc0eee4"
+  git_remote: "https://x-access-token:ghs_FhW4M4TmdkVUw8Om3VZ1e7pO685xf7028pZ3@github.com/viash-hub/demultiplex"
+  git_tag: "v0.3.3-3-ge6f8b20"
 package_config:
  name: "demultiplex"
-  version: "v0.3.3"
+  version: "v0.3.4"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -164,10 +169,12 @@ package_config:
  target: "target"
  config_mods:
  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
-    \ := '$id'\n"
+    \ := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n\
+    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
+    )'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.4'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/io/untar/main.nf
+++ b/target/nextflow/io/untar/main.nf
@@ -1,4 +1,4 @@
-// untar v0.3.3
+// untar v0.3.4
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2806,7 +2806,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "untar",
  "namespace" : "io",
-  "version" : "v0.3.3",
+  "version" : "v0.3.4",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -2866,6 +2866,11 @@ meta = [
      "type" : "bash_script",
      "path" : "script.sh",
      "is_executable" : true
+    },
+    {
+      "type" : "file",
+      "path" : "/src/config/labels.config",
+      "dest" : "nextflow_labels.config"
    }
  ],
  "description" : "Unpack a .tar file. When the contents of the .tar file is just a single directory,\nput the contents of the directory into the output folder instead of that directory.\n",
@@ -2954,7 +2959,10 @@ meta = [
          "cpu200" : "cpus = 200",
          "cpu500" : "cpus = 500",
          "cpu1000" : "cpus = 1000"
-        }
+        },
+        "script" : [
+          "includeConfig(\\"nextflow_labels.config\\")"
+        ]
      },
      "debug" : false,
      "container" : "docker"
@@ -2966,7 +2974,7 @@ meta = [
      "id" : "docker",
      "image" : "debian:stable-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.3.3",
+      "target_tag" : "v0.3.4",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -2989,13 +2997,13 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/untar",
    "viash_version" : "0.9.0",
-    "git_commit" : "e297e8ff45464065384476fe521ab2700ec3739c",
-    "git_remote" : "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.3.2-4-ge297e8f"
+    "git_commit" : "e6f8b20d70be8f47907c08cc3c7802920cc0eee4",
+    "git_remote" : "https://x-access-token:ghs_FhW4M4TmdkVUw8Om3VZ1e7pO685xf7028pZ3@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.3.3-3-ge6f8b20"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.3.3",
+    "version" : "v0.3.4",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -3009,10 +3017,10 @@ meta = [
    "source" : "src",
    "target" : "target",
    "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
+      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.3'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.4'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3465,7 +3473,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/demultiplex/io/untar",
-    "tag" : "v0.3.3"
+    "tag" : "v0.3.4"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/io/untar/nextflow.config
+++ b/target/nextflow/io/untar/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'io/untar'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.3.3'
+  version = 'v0.3.4'
  description = 'Unpack a .tar file. When the contents of the .tar file is just a single directory,\nput the contents of the directory into the output folder instead of that directory.\n'
 }

@@ -122,4 +122,4 @@ process{
  withLabel: cpu1000 { cpus = 1000 }
 }

-
+includeConfig("nextflow_labels.config")
--- a/target/nextflow/io/untar/nextflow_labels.config
+++ b/target/nextflow/io/untar/nextflow_labels.config
@@ -0,0 +1,98 @@
+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 {
+        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
+    }
+
+    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)
+    }
+  }
--- a/target/nextflow/runner/.config.vsh.yaml
+++ b/target/nextflow/runner/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "runner"
-version: "v0.3.3"
+version: "v0.3.4"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -89,6 +89,9 @@ resources:
  path: "main.nf"
  is_executable: true
  entrypoint: "run_wf"
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
 description: "Runner for demultiplexing of raw sequencing data"
 info: null
 status: "enabled"
@@ -165,6 +168,8 @@ runners:
      cpu200: "cpus = 200"
      cpu500: "cpus = 500"
      cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
  debug: false
  container: "docker"
 engines:
@@ -179,15 +184,15 @@ build_info:
  output: "target/nextflow/runner"
  executable: "target/nextflow/runner/main.nf"
  viash_version: "0.9.0"
-  git_commit: "e297e8ff45464065384476fe521ab2700ec3739c"
-  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.2-4-ge297e8f"
+  git_commit: "e6f8b20d70be8f47907c08cc3c7802920cc0eee4"
+  git_remote: "https://x-access-token:ghs_FhW4M4TmdkVUw8Om3VZ1e7pO685xf7028pZ3@github.com/viash-hub/demultiplex"
+  git_tag: "v0.3.3-3-ge6f8b20"
  dependencies:
  - "target/nextflow/demultiplex"
  - "target/nextflow/io/publish"
 package_config:
  name: "demultiplex"
-  version: "v0.3.3"
+  version: "v0.3.4"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -198,10 +203,12 @@ package_config:
  target: "target"
  config_mods:
  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
-    \ := '$id'\n"
+    \ := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n\
+    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
+    )'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.3'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.4'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/runner/main.nf
+++ b/target/nextflow/runner/main.nf
@@ -1,4 +1,4 @@
-// runner v0.3.3
+// runner v0.3.4
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2805,7 +2805,7 @@ meta = [
  "resources_dir": moduleDir.toRealPath().normalize(),
  "config": processConfig(readJsonBlob('''{
  "name" : "runner",
-  "version" : "v0.3.3",
+  "version" : "v0.3.4",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -2909,6 +2909,11 @@ meta = [
      "path" : "main.nf",
      "is_executable" : true,
      "entrypoint" : "run_wf"
+    },
+    {
+      "type" : "file",
+      "path" : "/src/config/labels.config",
+      "dest" : "nextflow_labels.config"
    }
  ],
  "description" : "Runner for demultiplexing of raw sequencing data",
@@ -2999,7 +3004,10 @@ meta = [
          "cpu200" : "cpus = 200",
          "cpu500" : "cpus = 500",
          "cpu1000" : "cpus = 1000"
-        }
+        },
+        "script" : [
+          "includeConfig(\\"nextflow_labels.config\\")"
+        ]
      },
      "debug" : false,
      "container" : "docker"
@@ -3021,13 +3029,13 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/runner",
    "viash_version" : "0.9.0",
-    "git_commit" : "e297e8ff45464065384476fe521ab2700ec3739c",
-    "git_remote" : "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.3.2-4-ge297e8f"
+    "git_commit" : "e6f8b20d70be8f47907c08cc3c7802920cc0eee4",
+    "git_remote" : "https://x-access-token:ghs_FhW4M4TmdkVUw8Om3VZ1e7pO685xf7028pZ3@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.3.3-3-ge6f8b20"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.3.3",
+    "version" : "v0.3.4",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -3041,10 +3049,10 @@ meta = [
    "source" : "src",
    "target" : "target",
    "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
+      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.3.3'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.4'"
    ],
    "keywords" : [
      "bioinformatics",
--- a/target/nextflow/runner/nextflow.config
+++ b/target/nextflow/runner/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'runner'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.3.3'
+  version = 'v0.3.4'
  description = 'Runner for demultiplexing of raw sequencing data'
 }

@@ -122,4 +122,4 @@ process{
  withLabel: cpu1000 { cpus = 1000 }
 }

-
+includeConfig("nextflow_labels.config")
--- a/target/nextflow/runner/nextflow_labels.config
+++ b/target/nextflow/runner/nextflow_labels.config
@@ -0,0 +1,98 @@
+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 {
+        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
+    }
+
+    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)
+    }
+  }