diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5f9d989..68ac6c0 100644
--- 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
diff --git a/_viash.yaml b/_viash.yaml
index 0cb9609..506cc23 100644
--- 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")'
diff --git a/target/executable/io/interop_summary_to_csv/.config.vsh.yaml b/target/executable/io/interop_summary_to_csv/.config.vsh.yaml
index e4ace00..9d115c2 100644
--- 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"
diff --git a/target/executable/io/interop_summary_to_csv/interop_summary_to_csv b/target/executable/io/interop_summary_to_csv/interop_summary_to_csv
index bfe2823..20f368c 100755
--- 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
diff --git a/target/executable/io/interop_summary_to_csv/nextflow_labels.config b/target/executable/io/interop_summary_to_csv/nextflow_labels.config
new file mode 100644
index 0000000..e7ab7b8
--- /dev/null
+++ 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)
+    }
+  }
diff --git a/target/executable/io/publish/.config.vsh.yaml b/target/executable/io/publish/.config.vsh.yaml
index d89e66f..bcfda71 100644
--- 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"
diff --git a/target/executable/io/publish/nextflow_labels.config b/target/executable/io/publish/nextflow_labels.config
new file mode 100644
index 0000000..e7ab7b8
--- /dev/null
+++ 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)
+    }
+  }
diff --git a/target/executable/io/publish/publish b/target/executable/io/publish/publish
index 9ac5fc3..2889720 100755
--- 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
diff --git a/target/executable/io/untar/.config.vsh.yaml b/target/executable/io/untar/.config.vsh.yaml
index 3b3d8a0..886ea7d 100644
--- 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"
diff --git a/target/executable/io/untar/nextflow_labels.config b/target/executable/io/untar/nextflow_labels.config
new file mode 100644
index 0000000..e7ab7b8
--- /dev/null
+++ 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)
+    }
+  }
diff --git a/target/executable/io/untar/untar b/target/executable/io/untar/untar
index a74f7a7..fa24fea 100755
--- 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
diff --git a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml
index 381c030..5395145 100644
--- 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"
diff --git a/target/nextflow/dataflow/combine_samples/main.nf b/target/nextflow/dataflow/combine_samples/main.nf
index f7575af..04a41c3 100644
--- 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",
diff --git a/target/nextflow/dataflow/combine_samples/nextflow.config b/target/nextflow/dataflow/combine_samples/nextflow.config
index 37d46e8..c23f949 100644
--- 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")
diff --git a/target/nextflow/dataflow/combine_samples/nextflow_labels.config b/target/nextflow/dataflow/combine_samples/nextflow_labels.config
new file mode 100644
index 0000000..e7ab7b8
--- /dev/null
+++ 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)
+    }
+  }
diff --git a/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml b/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml
index 8a63229..a0a1d5e 100644
--- 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"
diff --git a/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf b/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
index 83cd959..c34b193 100644
--- 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",
diff --git a/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow.config b/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow.config
index 3dca43a..3a2cc35 100644
--- 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")
diff --git a/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow_labels.config b/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow_labels.config
new file mode 100644
index 0000000..e7ab7b8
--- /dev/null
+++ 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)
+    }
+  }
diff --git a/target/nextflow/demultiplex/.config.vsh.yaml b/target/nextflow/demultiplex/.config.vsh.yaml
index ca29045..5a2a2e2 100644
--- 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"
diff --git a/target/nextflow/demultiplex/main.nf b/target/nextflow/demultiplex/main.nf
index b4b94d6..b713c1d 100644
--- 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",
diff --git a/target/nextflow/demultiplex/nextflow.config b/target/nextflow/demultiplex/nextflow.config
index 51af71b..b7a1762 100644
--- 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")
diff --git a/target/nextflow/demultiplex/nextflow_labels.config b/target/nextflow/demultiplex/nextflow_labels.config
new file mode 100644
index 0000000..e7ab7b8
--- /dev/null
+++ 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)
+    }
+  }
diff --git a/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml b/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml
index f589f95..3565d57 100644
--- 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"
diff --git a/target/nextflow/io/interop_summary_to_csv/main.nf b/target/nextflow/io/interop_summary_to_csv/main.nf
index a018462..f9a9b5a 100644
--- 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"
 }'''),
diff --git a/target/nextflow/io/interop_summary_to_csv/nextflow.config b/target/nextflow/io/interop_summary_to_csv/nextflow.config
index 8d86c58..f384448 100644
--- 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")
diff --git a/target/nextflow/io/interop_summary_to_csv/nextflow_labels.config b/target/nextflow/io/interop_summary_to_csv/nextflow_labels.config
new file mode 100644
index 0000000..e7ab7b8
--- /dev/null
+++ 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)
+    }
+  }
diff --git a/target/nextflow/io/publish/.config.vsh.yaml b/target/nextflow/io/publish/.config.vsh.yaml
index 4cd6e89..88fd47e 100644
--- 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"
diff --git a/target/nextflow/io/publish/main.nf b/target/nextflow/io/publish/main.nf
index 8d089e5..4a1ad03 100644
--- 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"
 }'''),
diff --git a/target/nextflow/io/publish/nextflow.config b/target/nextflow/io/publish/nextflow.config
index c96ca53..0cfd662 100644
--- 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")
diff --git a/target/nextflow/io/publish/nextflow_labels.config b/target/nextflow/io/publish/nextflow_labels.config
new file mode 100644
index 0000000..e7ab7b8
--- /dev/null
+++ 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)
+    }
+  }
diff --git a/target/nextflow/io/untar/.config.vsh.yaml b/target/nextflow/io/untar/.config.vsh.yaml
index 5a0c730..1c5560b 100644
--- 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"
diff --git a/target/nextflow/io/untar/main.nf b/target/nextflow/io/untar/main.nf
index 06664d1..4f0ae1d 100644
--- 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"
 }'''),
diff --git a/target/nextflow/io/untar/nextflow.config b/target/nextflow/io/untar/nextflow.config
index 44f0c79..564d4b7 100644
--- 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")
diff --git a/target/nextflow/io/untar/nextflow_labels.config b/target/nextflow/io/untar/nextflow_labels.config
new file mode 100644
index 0000000..e7ab7b8
--- /dev/null
+++ 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)
+    }
+  }
diff --git a/target/nextflow/runner/.config.vsh.yaml b/target/nextflow/runner/.config.vsh.yaml
index 4d79241..1840269 100644
--- 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"
diff --git a/target/nextflow/runner/main.nf b/target/nextflow/runner/main.nf
index d06ecec..b4cc445 100644
--- 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",
diff --git a/target/nextflow/runner/nextflow.config b/target/nextflow/runner/nextflow.config
index 1fc1d9f..153f65f 100644
--- 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")
diff --git a/target/nextflow/runner/nextflow_labels.config b/target/nextflow/runner/nextflow_labels.config
new file mode 100644
index 0000000..e7ab7b8
--- /dev/null
+++ 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)
+    }
+  }