Build branch main with version main (d7d3b3e)

Build pipeline: viash-hub.demultiplex.main-6k4dk

Source commit: d7d3b3e1de

Source message: Automatically include resources labels during build (#32)

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

_viash.yaml

@@ -16,3 +16,5 @@ 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")'

target/executable/io/interop_summary_to_csv/.config.vsh.yaml

@@ -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:
@@ -141,9 +146,9 @@ 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: "798e361afeea8dbb84dc23ef38e4fbc3883463e7"
-  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-13-g798e361"
+  git_commit: "d7d3b3e1de64f07a8b161b68a60098103ff691fb"
+  git_remote: "https://x-access-token:ghs_VevxXQvu4BBoh9Z4GlymTfE1DeHryU1sU0kQ@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-14-gd7d3b3e"
 package_config:
   name: "demultiplex"
   version: "main"
@@ -157,7 +162,9 @@ 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 := 'main'"

target/executable/io/interop_summary_to_csv/interop_summary_to_csv

@@ -470,9 +470,9 @@ 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="2024-12-19T15:39:33Z"
+LABEL org.opencontainers.image.created="2024-12-20T11:16:00Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="798e361afeea8dbb84dc23ef38e4fbc3883463e7"
+LABEL org.opencontainers.image.revision="d7d3b3e1de64f07a8b161b68a60098103ff691fb"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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)
+    }
+  }

target/executable/io/publish/.config.vsh.yaml

@@ -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:
@@ -191,9 +196,9 @@ build_info:
   output: "target/executable/io/publish"
   executable: "target/executable/io/publish/publish"
   viash_version: "0.9.0"
-  git_commit: "798e361afeea8dbb84dc23ef38e4fbc3883463e7"
-  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-13-g798e361"
+  git_commit: "d7d3b3e1de64f07a8b161b68a60098103ff691fb"
+  git_remote: "https://x-access-token:ghs_VevxXQvu4BBoh9Z4GlymTfE1DeHryU1sU0kQ@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-14-gd7d3b3e"
 package_config:
   name: "demultiplex"
   version: "main"
@@ -207,7 +212,9 @@ 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 := 'main'"

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)
+    }
+  }

target/executable/io/publish/publish

@@ -490,9 +490,9 @@ 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="2024-12-19T15:39:33Z"
+LABEL org.opencontainers.image.created="2024-12-20T11:16:00Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="798e361afeea8dbb84dc23ef38e4fbc3883463e7"
+LABEL org.opencontainers.image.revision="d7d3b3e1de64f07a8b161b68a60098103ff691fb"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/io/untar/.config.vsh.yaml

@@ -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:
@@ -148,9 +153,9 @@ build_info:
   output: "target/executable/io/untar"
   executable: "target/executable/io/untar/untar"
   viash_version: "0.9.0"
-  git_commit: "798e361afeea8dbb84dc23ef38e4fbc3883463e7"
-  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-13-g798e361"
+  git_commit: "d7d3b3e1de64f07a8b161b68a60098103ff691fb"
+  git_remote: "https://x-access-token:ghs_VevxXQvu4BBoh9Z4GlymTfE1DeHryU1sU0kQ@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-14-gd7d3b3e"
 package_config:
   name: "demultiplex"
   version: "main"
@@ -164,7 +169,9 @@ 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 := 'main'"

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)
+    }
+  }

target/executable/io/untar/untar

@@ -476,9 +476,9 @@ 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="2024-12-19T15:39:34Z"
+LABEL org.opencontainers.image.created="2024-12-20T11:16:01Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="798e361afeea8dbb84dc23ef38e4fbc3883463e7"
+LABEL org.opencontainers.image.revision="d7d3b3e1de64f07a8b161b68a60098103ff691fb"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/nextflow/dataflow/combine_samples/.config.vsh.yaml

@@ -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:
@@ -139,9 +144,9 @@ build_info:
   output: "target/nextflow/dataflow/combine_samples"
   executable: "target/nextflow/dataflow/combine_samples/main.nf"
   viash_version: "0.9.0"
-  git_commit: "798e361afeea8dbb84dc23ef38e4fbc3883463e7"
-  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-13-g798e361"
+  git_commit: "d7d3b3e1de64f07a8b161b68a60098103ff691fb"
+  git_remote: "https://x-access-token:ghs_VevxXQvu4BBoh9Z4GlymTfE1DeHryU1sU0kQ@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-14-gd7d3b3e"
 package_config:
   name: "demultiplex"
   version: "main"
@@ -155,7 +160,9 @@ 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 := 'main'"

target/nextflow/dataflow/combine_samples/main.nf

@@ -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"
@@ -2972,9 +2980,9 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/dataflow/combine_samples",
     "viash_version" : "0.9.0",
-    "git_commit" : "798e361afeea8dbb84dc23ef38e4fbc3883463e7",
-    "git_remote" : "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-13-g798e361"
+    "git_commit" : "d7d3b3e1de64f07a8b161b68a60098103ff691fb",
+    "git_remote" : "https://x-access-token:ghs_VevxXQvu4BBoh9Z4GlymTfE1DeHryU1sU0kQ@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.1.1-14-gd7d3b3e"
   },
   "package_config" : {
     "name" : "demultiplex",
@@ -2992,7 +3000,7 @@ 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 := 'main'"

target/nextflow/dataflow/combine_samples/nextflow.config

@@ -122,4 +122,4 @@ process{
   withLabel: cpu1000 { cpus = 1000 }
 }
 
-
+includeConfig("nextflow_labels.config")

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)
+    }
+  }

target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml

@@ -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:
@@ -133,9 +138,9 @@ 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: "798e361afeea8dbb84dc23ef38e4fbc3883463e7"
-  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-13-g798e361"
+  git_commit: "d7d3b3e1de64f07a8b161b68a60098103ff691fb"
+  git_remote: "https://x-access-token:ghs_VevxXQvu4BBoh9Z4GlymTfE1DeHryU1sU0kQ@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-14-gd7d3b3e"
 package_config:
   name: "demultiplex"
   version: "main"
@@ -149,7 +154,9 @@ 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 := 'main'"

target/nextflow/dataflow/gather_fastqs_and_validate/main.nf

@@ -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"
@@ -2965,9 +2973,9 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/dataflow/gather_fastqs_and_validate",
     "viash_version" : "0.9.0",
-    "git_commit" : "798e361afeea8dbb84dc23ef38e4fbc3883463e7",
-    "git_remote" : "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-13-g798e361"
+    "git_commit" : "d7d3b3e1de64f07a8b161b68a60098103ff691fb",
+    "git_remote" : "https://x-access-token:ghs_VevxXQvu4BBoh9Z4GlymTfE1DeHryU1sU0kQ@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.1.1-14-gd7d3b3e"
   },
   "package_config" : {
     "name" : "demultiplex",
@@ -2985,7 +2993,7 @@ 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 := 'main'"

target/nextflow/dataflow/gather_fastqs_and_validate/nextflow.config

@@ -122,4 +122,4 @@ process{
   withLabel: cpu1000 { cpus = 1000 }
 }
 
-
+includeConfig("nextflow_labels.config")

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)
+    }
+  }

target/nextflow/demultiplex/.config.vsh.yaml

@@ -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: "798e361afeea8dbb84dc23ef38e4fbc3883463e7"
-  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-13-g798e361"
+  git_commit: "d7d3b3e1de64f07a8b161b68a60098103ff691fb"
+  git_remote: "https://x-access-token:ghs_VevxXQvu4BBoh9Z4GlymTfE1DeHryU1sU0kQ@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-14-gd7d3b3e"
   dependencies:
   - "target/nextflow/io/untar"
   - "target/nextflow/dataflow/gather_fastqs_and_validate"
@@ -256,7 +261,9 @@ 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 := 'main'"

target/nextflow/demultiplex/main.nf

@@ -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"
@@ -3101,9 +3109,9 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/demultiplex",
     "viash_version" : "0.9.0",
-    "git_commit" : "798e361afeea8dbb84dc23ef38e4fbc3883463e7",
-    "git_remote" : "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-13-g798e361"
+    "git_commit" : "d7d3b3e1de64f07a8b161b68a60098103ff691fb",
+    "git_remote" : "https://x-access-token:ghs_VevxXQvu4BBoh9Z4GlymTfE1DeHryU1sU0kQ@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.1.1-14-gd7d3b3e"
   },
   "package_config" : {
     "name" : "demultiplex",
@@ -3121,7 +3129,7 @@ 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 := 'main'"

target/nextflow/demultiplex/nextflow.config

@@ -122,4 +122,4 @@ process{
   withLabel: cpu1000 { cpus = 1000 }
 }
 
-
+includeConfig("nextflow_labels.config")

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)
+    }
+  }

target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml

@@ -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:
@@ -141,9 +146,9 @@ 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: "798e361afeea8dbb84dc23ef38e4fbc3883463e7"
-  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-13-g798e361"
+  git_commit: "d7d3b3e1de64f07a8b161b68a60098103ff691fb"
+  git_remote: "https://x-access-token:ghs_VevxXQvu4BBoh9Z4GlymTfE1DeHryU1sU0kQ@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-14-gd7d3b3e"
 package_config:
   name: "demultiplex"
   version: "main"
@@ -157,7 +162,9 @@ 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 := 'main'"

target/nextflow/io/interop_summary_to_csv/main.nf

@@ -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"
@@ -2977,9 +2985,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/interop_summary_to_csv",
     "viash_version" : "0.9.0",
-    "git_commit" : "798e361afeea8dbb84dc23ef38e4fbc3883463e7",
-    "git_remote" : "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-13-g798e361"
+    "git_commit" : "d7d3b3e1de64f07a8b161b68a60098103ff691fb",
+    "git_remote" : "https://x-access-token:ghs_VevxXQvu4BBoh9Z4GlymTfE1DeHryU1sU0kQ@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.1.1-14-gd7d3b3e"
   },
   "package_config" : {
     "name" : "demultiplex",
@@ -2997,7 +3005,7 @@ 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 := 'main'"

target/nextflow/io/interop_summary_to_csv/nextflow.config

@@ -121,4 +121,4 @@ process{
   withLabel: cpu1000 { cpus = 1000 }
 }
 
-
+includeConfig("nextflow_labels.config")

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)
+    }
+  }

target/nextflow/io/publish/.config.vsh.yaml

@@ -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:
@@ -191,9 +196,9 @@ build_info:
   output: "target/nextflow/io/publish"
   executable: "target/nextflow/io/publish/main.nf"
   viash_version: "0.9.0"
-  git_commit: "798e361afeea8dbb84dc23ef38e4fbc3883463e7"
-  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-13-g798e361"
+  git_commit: "d7d3b3e1de64f07a8b161b68a60098103ff691fb"
+  git_remote: "https://x-access-token:ghs_VevxXQvu4BBoh9Z4GlymTfE1DeHryU1sU0kQ@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-14-gd7d3b3e"
 package_config:
   name: "demultiplex"
   version: "main"
@@ -207,7 +212,9 @@ 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 := 'main'"

target/nextflow/io/publish/main.nf

@@ -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"
@@ -3036,9 +3044,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/publish",
     "viash_version" : "0.9.0",
-    "git_commit" : "798e361afeea8dbb84dc23ef38e4fbc3883463e7",
-    "git_remote" : "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-13-g798e361"
+    "git_commit" : "d7d3b3e1de64f07a8b161b68a60098103ff691fb",
+    "git_remote" : "https://x-access-token:ghs_VevxXQvu4BBoh9Z4GlymTfE1DeHryU1sU0kQ@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.1.1-14-gd7d3b3e"
   },
   "package_config" : {
     "name" : "demultiplex",
@@ -3056,7 +3064,7 @@ 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 := 'main'"

target/nextflow/io/publish/nextflow.config

@@ -122,4 +122,4 @@ process{
   withLabel: cpu1000 { cpus = 1000 }
 }
 
-
+includeConfig("nextflow_labels.config")

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)
+    }
+  }

target/nextflow/io/untar/.config.vsh.yaml

@@ -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:
@@ -148,9 +153,9 @@ build_info:
   output: "target/nextflow/io/untar"
   executable: "target/nextflow/io/untar/main.nf"
   viash_version: "0.9.0"
-  git_commit: "798e361afeea8dbb84dc23ef38e4fbc3883463e7"
-  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-13-g798e361"
+  git_commit: "d7d3b3e1de64f07a8b161b68a60098103ff691fb"
+  git_remote: "https://x-access-token:ghs_VevxXQvu4BBoh9Z4GlymTfE1DeHryU1sU0kQ@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-14-gd7d3b3e"
 package_config:
   name: "demultiplex"
   version: "main"
@@ -164,7 +169,9 @@ 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 := 'main'"

target/nextflow/io/untar/main.nf

@@ -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"
@@ -2989,9 +2997,9 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/untar",
     "viash_version" : "0.9.0",
-    "git_commit" : "798e361afeea8dbb84dc23ef38e4fbc3883463e7",
-    "git_remote" : "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-13-g798e361"
+    "git_commit" : "d7d3b3e1de64f07a8b161b68a60098103ff691fb",
+    "git_remote" : "https://x-access-token:ghs_VevxXQvu4BBoh9Z4GlymTfE1DeHryU1sU0kQ@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.1.1-14-gd7d3b3e"
   },
   "package_config" : {
     "name" : "demultiplex",
@@ -3009,7 +3017,7 @@ 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 := 'main'"

target/nextflow/io/untar/nextflow.config

@@ -122,4 +122,4 @@ process{
   withLabel: cpu1000 { cpus = 1000 }
 }
 
-
+includeConfig("nextflow_labels.config")

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)
+    }
+  }

target/nextflow/runner/.config.vsh.yaml

@@ -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:
@@ -179,9 +184,9 @@ build_info:
   output: "target/nextflow/runner"
   executable: "target/nextflow/runner/main.nf"
   viash_version: "0.9.0"
-  git_commit: "798e361afeea8dbb84dc23ef38e4fbc3883463e7"
-  git_remote: "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-13-g798e361"
+  git_commit: "d7d3b3e1de64f07a8b161b68a60098103ff691fb"
+  git_remote: "https://x-access-token:ghs_VevxXQvu4BBoh9Z4GlymTfE1DeHryU1sU0kQ@github.com/viash-hub/demultiplex"
+  git_tag: "v0.1.1-14-gd7d3b3e"
   dependencies:
   - "target/nextflow/demultiplex"
   - "target/nextflow/io/publish"
@@ -198,7 +203,9 @@ 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 := 'main'"

target/nextflow/runner/main.nf

@@ -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"
@@ -3021,9 +3029,9 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/runner",
     "viash_version" : "0.9.0",
-    "git_commit" : "798e361afeea8dbb84dc23ef38e4fbc3883463e7",
-    "git_remote" : "https://x-access-token:ghs_44flLTQIYGBkc9xcwCZoLYe7mxXzgw1iszFO@github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-13-g798e361"
+    "git_commit" : "d7d3b3e1de64f07a8b161b68a60098103ff691fb",
+    "git_remote" : "https://x-access-token:ghs_VevxXQvu4BBoh9Z4GlymTfE1DeHryU1sU0kQ@github.com/viash-hub/demultiplex",
+    "git_tag" : "v0.1.1-14-gd7d3b3e"
   },
   "package_config" : {
     "name" : "demultiplex",
@@ -3041,7 +3049,7 @@ 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 := 'main'"

target/nextflow/runner/nextflow.config

@@ -122,4 +122,4 @@ process{
   withLabel: cpu1000 { cpus = 1000 }
 }
 
-
+includeConfig("nextflow_labels.config")

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)
+    }
+  }