Build branch main with version main (4adb388)

Build pipeline: viash-hub.rnaseq.main-c9pqm

Source commit: 4adb388c7d

Source message: Merge pull request #29 from viash-hub/add-labels

Add labels (and then some)

target/nextflow/bedtools_genomecov/.config.vsh.yaml

@@ -63,6 +63,9 @@ resources:
 - type: "bash_script"
   path: "script.sh"
   is_executable: true
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
 description: "Compute BEDGRAPH (-bg) summaries of feature coverage"
 test_resources:
 - type: "bash_script"
@@ -152,6 +155,8 @@ runners:
       cpu200: "cpus = 200"
       cpu500: "cpus = 500"
       cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
   debug: false
   container: "docker"
 engines:
@@ -178,8 +183,8 @@ build_info:
   output: "target/nextflow/bedtools_genomecov"
   executable: "target/nextflow/bedtools_genomecov/main.nf"
   viash_version: "0.9.0"
-  git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
-  git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+  git_commit: "4adb388c7d928eea02bccf890214f3b932b08714"
+  git_remote: "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"
@@ -200,8 +205,10 @@ package_config:
   source: "src"
   target: "target"
   config_mods:
-  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
-    \ := '$id'\n"
+  - ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config',\
+    \ dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag\
+    \ := '$id'\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/bedtools_genomecov/main.nf

@@ -2886,6 +2886,11 @@ meta = [
       "type" : "bash_script",
       "path" : "script.sh",
       "is_executable" : true
+    },
+    {
+      "type" : "file",
+      "path" : "/src/workflows/utils/labels.config",
+      "dest" : "nextflow_labels.config"
     }
   ],
   "description" : "Compute BEDGRAPH (-bg) summaries of feature coverage",
@@ -2997,7 +3002,10 @@ meta = [
           "cpu200" : "cpus = 200",
           "cpu500" : "cpus = 500",
           "cpu1000" : "cpus = 1000"
-        }
+        },
+        "script" : [
+          "includeConfig(\\"nextflow_labels.config\\")"
+        ]
       },
       "debug" : false,
       "container" : "docker"
@@ -3031,8 +3039,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/bedtools_genomecov",
     "viash_version" : "0.9.0",
-    "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e",
-    "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+    "git_commit" : "4adb388c7d928eea02bccf890214f3b932b08714",
+    "git_remote" : "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",
@@ -3063,7 +3071,7 @@ meta = [
     "source" : "/workdir/root/repo/src",
     "target" : "/workdir/root/repo/target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
+      ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag := '$id'\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/bedtools_genomecov/nextflow.config

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

target/nextflow/bedtools_genomecov/nextflow_labels.config

@@ -0,0 +1,44 @@
+process {
+  // Default resources for components that hardly do any processing
+  memory = { 2.GB * task.attempt }
+  cpus = 1
+
+  // Retry for exit codes that have something to do with memory issues
+  errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
+  maxRetries = 3
+  maxMemory = null
+
+  // Resource labels
+  withLabel: singlecpu { cpus = 1 }
+  withLabel: lowcpu { cpus = 2 }
+  withLabel: midcpu { cpus = 4 }
+  withLabel: highcpu { cpus = 8 }
+  withLabel: veryhighcpu { cpus = 16 }
+ 
+  withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 24.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 48.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/cat_additional_fasta/.config.vsh.yaml

@@ -69,6 +69,9 @@ resources:
 - type: "python_script"
   path: "script.py"
   is_executable: true
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
 description: "Concatenate addional fasta file to reference FASTA and GTF files.\n"
 test_resources:
 - type: "bash_script"
@@ -162,6 +165,8 @@ runners:
       cpu200: "cpus = 200"
       cpu500: "cpus = 500"
       cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
   debug: false
   container: "docker"
 engines:
@@ -182,8 +187,8 @@ build_info:
   output: "target/nextflow/cat_additional_fasta"
   executable: "target/nextflow/cat_additional_fasta/main.nf"
   viash_version: "0.9.0"
-  git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
-  git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+  git_commit: "4adb388c7d928eea02bccf890214f3b932b08714"
+  git_remote: "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"
@@ -204,8 +209,10 @@ package_config:
   source: "src"
   target: "target"
   config_mods:
-  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
-    \ := '$id'\n"
+  - ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config',\
+    \ dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag\
+    \ := '$id'\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/cat_additional_fasta/main.nf

@@ -2887,6 +2887,11 @@ meta = [
       "type" : "python_script",
       "path" : "script.py",
       "is_executable" : true
+    },
+    {
+      "type" : "file",
+      "path" : "/src/workflows/utils/labels.config",
+      "dest" : "nextflow_labels.config"
     }
   ],
   "description" : "Concatenate addional fasta file to reference FASTA and GTF files.\n",
@@ -3006,7 +3011,10 @@ meta = [
           "cpu200" : "cpus = 200",
           "cpu500" : "cpus = 500",
           "cpu1000" : "cpus = 1000"
-        }
+        },
+        "script" : [
+          "includeConfig(\\"nextflow_labels.config\\")"
+        ]
       },
       "debug" : false,
       "container" : "docker"
@@ -3032,8 +3040,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/cat_additional_fasta",
     "viash_version" : "0.9.0",
-    "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e",
-    "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+    "git_commit" : "4adb388c7d928eea02bccf890214f3b932b08714",
+    "git_remote" : "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",
@@ -3064,7 +3072,7 @@ meta = [
     "source" : "/workdir/root/repo/src",
     "target" : "/workdir/root/repo/target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
+      ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag := '$id'\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/cat_additional_fasta/nextflow.config

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

target/nextflow/cat_additional_fasta/nextflow_labels.config

@@ -0,0 +1,44 @@
+process {
+  // Default resources for components that hardly do any processing
+  memory = { 2.GB * task.attempt }
+  cpus = 1
+
+  // Retry for exit codes that have something to do with memory issues
+  errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
+  maxRetries = 3
+  maxMemory = null
+
+  // Resource labels
+  withLabel: singlecpu { cpus = 1 }
+  withLabel: lowcpu { cpus = 2 }
+  withLabel: midcpu { cpus = 4 }
+  withLabel: highcpu { cpus = 8 }
+  withLabel: veryhighcpu { cpus = 16 }
+ 
+  withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 24.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 48.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/cat_fastq/.config.vsh.yaml

@@ -53,6 +53,9 @@ resources:
 - type: "bash_script"
   path: "script.sh"
   is_executable: true
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
 description: "Concatenate multiple fastq files"
 test_resources:
 - type: "bash_script"
@@ -149,6 +152,8 @@ runners:
       cpu200: "cpus = 200"
       cpu500: "cpus = 500"
       cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
   debug: false
   container: "docker"
 engines:
@@ -169,8 +174,8 @@ build_info:
   output: "target/nextflow/cat_fastq"
   executable: "target/nextflow/cat_fastq/main.nf"
   viash_version: "0.9.0"
-  git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
-  git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+  git_commit: "4adb388c7d928eea02bccf890214f3b932b08714"
+  git_remote: "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"
@@ -191,8 +196,10 @@ package_config:
   source: "src"
   target: "target"
   config_mods:
-  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
-    \ := '$id'\n"
+  - ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config',\
+    \ dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag\
+    \ := '$id'\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/cat_fastq/main.nf

@@ -2873,6 +2873,11 @@ meta = [
       "type" : "bash_script",
       "path" : "script.sh",
       "is_executable" : true
+    },
+    {
+      "type" : "file",
+      "path" : "/src/workflows/utils/labels.config",
+      "dest" : "nextflow_labels.config"
     }
   ],
   "description" : "Concatenate multiple fastq files",
@@ -2997,7 +3002,10 @@ meta = [
           "cpu200" : "cpus = 200",
           "cpu500" : "cpus = 500",
           "cpu1000" : "cpus = 1000"
-        }
+        },
+        "script" : [
+          "includeConfig(\\"nextflow_labels.config\\")"
+        ]
       },
       "debug" : false,
       "container" : "docker"
@@ -3023,8 +3031,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/cat_fastq",
     "viash_version" : "0.9.0",
-    "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e",
-    "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+    "git_commit" : "4adb388c7d928eea02bccf890214f3b932b08714",
+    "git_remote" : "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",
@@ -3055,7 +3063,7 @@ meta = [
     "source" : "/workdir/root/repo/src",
     "target" : "/workdir/root/repo/target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
+      ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag := '$id'\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/cat_fastq/nextflow.config

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

target/nextflow/cat_fastq/nextflow_labels.config

@@ -0,0 +1,44 @@
+process {
+  // Default resources for components that hardly do any processing
+  memory = { 2.GB * task.attempt }
+  cpus = 1
+
+  // Retry for exit codes that have something to do with memory issues
+  errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
+  maxRetries = 3
+  maxMemory = null
+
+  // Resource labels
+  withLabel: singlecpu { cpus = 1 }
+  withLabel: lowcpu { cpus = 2 }
+  withLabel: midcpu { cpus = 4 }
+  withLabel: highcpu { cpus = 8 }
+  withLabel: veryhighcpu { cpus = 16 }
+ 
+  withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 24.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 48.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/deseq2_qc/.config.vsh.yaml

@@ -115,6 +115,9 @@ resources:
   path: "deseq2_pca_header.txt"
 - type: "file"
   path: "deseq2_clustering_header.txt"
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
 description: "run deseq2, perform pca, generate heatmaps and scatterplots for samples\
   \ in the counts files\n"
 test_resources:
@@ -205,6 +208,8 @@ runners:
       cpu200: "cpus = 200"
       cpu500: "cpus = 500"
       cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
   debug: false
   container: "docker"
 engines:
@@ -237,8 +242,8 @@ build_info:
   output: "target/nextflow/deseq2_qc"
   executable: "target/nextflow/deseq2_qc/main.nf"
   viash_version: "0.9.0"
-  git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
-  git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+  git_commit: "4adb388c7d928eea02bccf890214f3b932b08714"
+  git_remote: "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"
@@ -259,8 +264,10 @@ package_config:
   source: "src"
   target: "target"
   config_mods:
-  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
-    \ := '$id'\n"
+  - ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config',\
+    \ dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag\
+    \ := '$id'\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/deseq2_qc/main.nf

@@ -2950,6 +2950,11 @@ meta = [
     {
       "type" : "file",
       "path" : "deseq2_clustering_header.txt"
+    },
+    {
+      "type" : "file",
+      "path" : "/src/workflows/utils/labels.config",
+      "dest" : "nextflow_labels.config"
     }
   ],
   "description" : "run deseq2, perform pca, generate heatmaps and scatterplots for samples in the counts files\n",
@@ -3061,7 +3066,10 @@ meta = [
           "cpu200" : "cpus = 200",
           "cpu500" : "cpus = 500",
           "cpu1000" : "cpus = 1000"
-        }
+        },
+        "script" : [
+          "includeConfig(\\"nextflow_labels.config\\")"
+        ]
       },
       "debug" : false,
       "container" : "docker"
@@ -3104,8 +3112,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/deseq2_qc",
     "viash_version" : "0.9.0",
-    "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e",
-    "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+    "git_commit" : "4adb388c7d928eea02bccf890214f3b932b08714",
+    "git_remote" : "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",
@@ -3136,7 +3144,7 @@ meta = [
     "source" : "/workdir/root/repo/src",
     "target" : "/workdir/root/repo/target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
+      ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag := '$id'\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/deseq2_qc/nextflow.config

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

target/nextflow/deseq2_qc/nextflow_labels.config

@@ -0,0 +1,44 @@
+process {
+  // Default resources for components that hardly do any processing
+  memory = { 2.GB * task.attempt }
+  cpus = 1
+
+  // Retry for exit codes that have something to do with memory issues
+  errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
+  maxRetries = 3
+  maxMemory = null
+
+  // Resource labels
+  withLabel: singlecpu { cpus = 1 }
+  withLabel: lowcpu { cpus = 2 }
+  withLabel: midcpu { cpus = 4 }
+  withLabel: highcpu { cpus = 8 }
+  withLabel: veryhighcpu { cpus = 16 }
+ 
+  withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 24.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 48.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/dupradar/.config.vsh.yaml

@@ -146,6 +146,9 @@ resources:
   is_executable: true
 - type: "file"
   path: "dupradar.r"
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
 description: "Assessment of duplication rates in RNA-Seq datasets\n"
 test_resources:
 - type: "bash_script"
@@ -237,6 +240,8 @@ runners:
       cpu200: "cpus = 200"
       cpu500: "cpus = 500"
       cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
   debug: false
   container: "docker"
 engines:
@@ -266,8 +271,8 @@ build_info:
   output: "target/nextflow/dupradar"
   executable: "target/nextflow/dupradar/main.nf"
   viash_version: "0.9.0"
-  git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
-  git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+  git_commit: "4adb388c7d928eea02bccf890214f3b932b08714"
+  git_remote: "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"
@@ -288,8 +293,10 @@ package_config:
   source: "src"
   target: "target"
   config_mods:
-  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
-    \ := '$id'\n"
+  - ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config',\
+    \ dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag\
+    \ := '$id'\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/dupradar/main.nf

@@ -2979,6 +2979,11 @@ meta = [
     {
       "type" : "file",
       "path" : "dupradar.r"
+    },
+    {
+      "type" : "file",
+      "path" : "/src/workflows/utils/labels.config",
+      "dest" : "nextflow_labels.config"
     }
   ],
   "description" : "Assessment of duplication rates in RNA-Seq datasets\n",
@@ -3094,7 +3099,10 @@ meta = [
           "cpu200" : "cpus = 200",
           "cpu500" : "cpus = 500",
           "cpu1000" : "cpus = 1000"
-        }
+        },
+        "script" : [
+          "includeConfig(\\"nextflow_labels.config\\")"
+        ]
       },
       "debug" : false,
       "container" : "docker"
@@ -3136,8 +3144,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/dupradar",
     "viash_version" : "0.9.0",
-    "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e",
-    "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+    "git_commit" : "4adb388c7d928eea02bccf890214f3b932b08714",
+    "git_remote" : "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",
@@ -3168,7 +3176,7 @@ meta = [
     "source" : "/workdir/root/repo/src",
     "target" : "/workdir/root/repo/target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
+      ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag := '$id'\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/dupradar/nextflow.config

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

target/nextflow/dupradar/nextflow_labels.config

@@ -0,0 +1,44 @@
+process {
+  // Default resources for components that hardly do any processing
+  memory = { 2.GB * task.attempt }
+  cpus = 1
+
+  // Retry for exit codes that have something to do with memory issues
+  errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
+  maxRetries = 3
+  maxMemory = null
+
+  // Resource labels
+  withLabel: singlecpu { cpus = 1 }
+  withLabel: lowcpu { cpus = 2 }
+  withLabel: midcpu { cpus = 4 }
+  withLabel: highcpu { cpus = 8 }
+  withLabel: veryhighcpu { cpus = 16 }
+ 
+  withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 24.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 48.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/getchromsizes/.config.vsh.yaml

@@ -49,6 +49,9 @@ resources:
 - type: "bash_script"
   path: "script.sh"
   is_executable: true
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
 description: "Generates a FASTA file of chromosome sizes and a fasta index file.\n"
 test_resources:
 - type: "bash_script"
@@ -139,6 +142,8 @@ runners:
       cpu200: "cpus = 200"
       cpu500: "cpus = 500"
       cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
   debug: false
   container: "docker"
 engines:
@@ -167,8 +172,8 @@ build_info:
   output: "target/nextflow/getchromsizes"
   executable: "target/nextflow/getchromsizes/main.nf"
   viash_version: "0.9.0"
-  git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
-  git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+  git_commit: "4adb388c7d928eea02bccf890214f3b932b08714"
+  git_remote: "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"
@@ -189,8 +194,10 @@ package_config:
   source: "src"
   target: "target"
   config_mods:
-  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
-    \ := '$id'\n"
+  - ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config',\
+    \ dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag\
+    \ := '$id'\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/getchromsizes/main.nf

@@ -2867,6 +2867,11 @@ meta = [
       "type" : "bash_script",
       "path" : "script.sh",
       "is_executable" : true
+    },
+    {
+      "type" : "file",
+      "path" : "/src/workflows/utils/labels.config",
+      "dest" : "nextflow_labels.config"
     }
   ],
   "description" : "Generates a FASTA file of chromosome sizes and a fasta index file.\n",
@@ -2979,7 +2984,10 @@ meta = [
           "cpu200" : "cpus = 200",
           "cpu500" : "cpus = 500",
           "cpu1000" : "cpus = 1000"
-        }
+        },
+        "script" : [
+          "includeConfig(\\"nextflow_labels.config\\")"
+        ]
       },
       "debug" : false,
       "container" : "docker"
@@ -3013,8 +3021,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/getchromsizes",
     "viash_version" : "0.9.0",
-    "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e",
-    "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+    "git_commit" : "4adb388c7d928eea02bccf890214f3b932b08714",
+    "git_remote" : "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",
@@ -3045,7 +3053,7 @@ meta = [
     "source" : "/workdir/root/repo/src",
     "target" : "/workdir/root/repo/target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
+      ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag := '$id'\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/getchromsizes/nextflow.config

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

target/nextflow/getchromsizes/nextflow_labels.config

@@ -0,0 +1,44 @@
+process {
+  // Default resources for components that hardly do any processing
+  memory = { 2.GB * task.attempt }
+  cpus = 1
+
+  // Retry for exit codes that have something to do with memory issues
+  errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
+  maxRetries = 3
+  maxMemory = null
+
+  // Resource labels
+  withLabel: singlecpu { cpus = 1 }
+  withLabel: lowcpu { cpus = 2 }
+  withLabel: midcpu { cpus = 4 }
+  withLabel: highcpu { cpus = 8 }
+  withLabel: veryhighcpu { cpus = 16 }
+ 
+  withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 24.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 48.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/gtf2bed/.config.vsh.yaml

@@ -31,6 +31,9 @@ resources:
   is_executable: true
 - type: "file"
   path: "gtf2bed.pl"
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
 description: "Create BED annotation file from GTF.\n"
 test_resources:
 - type: "bash_script"
@@ -120,6 +123,8 @@ runners:
       cpu200: "cpus = 200"
       cpu500: "cpus = 500"
       cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
   debug: false
   container: "docker"
 engines:
@@ -145,8 +150,8 @@ build_info:
   output: "target/nextflow/gtf2bed"
   executable: "target/nextflow/gtf2bed/main.nf"
   viash_version: "0.9.0"
-  git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
-  git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+  git_commit: "4adb388c7d928eea02bccf890214f3b932b08714"
+  git_remote: "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"
@@ -167,8 +172,10 @@ package_config:
   source: "src"
   target: "target"
   config_mods:
-  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
-    \ := '$id'\n"
+  - ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config',\
+    \ dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag\
+    \ := '$id'\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/gtf2bed/main.nf

@@ -2849,6 +2849,11 @@ meta = [
     {
       "type" : "file",
       "path" : "gtf2bed.pl"
+    },
+    {
+      "type" : "file",
+      "path" : "/src/workflows/utils/labels.config",
+      "dest" : "nextflow_labels.config"
     }
   ],
   "description" : "Create BED annotation file from GTF.\n",
@@ -2960,7 +2965,10 @@ meta = [
           "cpu200" : "cpus = 200",
           "cpu500" : "cpus = 500",
           "cpu1000" : "cpus = 1000"
-        }
+        },
+        "script" : [
+          "includeConfig(\\"nextflow_labels.config\\")"
+        ]
       },
       "debug" : false,
       "container" : "docker"
@@ -2995,8 +3003,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/gtf2bed",
     "viash_version" : "0.9.0",
-    "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e",
-    "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+    "git_commit" : "4adb388c7d928eea02bccf890214f3b932b08714",
+    "git_remote" : "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",
@@ -3027,7 +3035,7 @@ meta = [
     "source" : "/workdir/root/repo/src",
     "target" : "/workdir/root/repo/target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
+      ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag := '$id'\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/gtf2bed/nextflow.config

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

target/nextflow/gtf2bed/nextflow_labels.config

@@ -0,0 +1,44 @@
+process {
+  // Default resources for components that hardly do any processing
+  memory = { 2.GB * task.attempt }
+  cpus = 1
+
+  // Retry for exit codes that have something to do with memory issues
+  errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
+  maxRetries = 3
+  maxMemory = null
+
+  // Resource labels
+  withLabel: singlecpu { cpus = 1 }
+  withLabel: lowcpu { cpus = 2 }
+  withLabel: midcpu { cpus = 4 }
+  withLabel: highcpu { cpus = 8 }
+  withLabel: veryhighcpu { cpus = 16 }
+ 
+  withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 24.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 48.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/gtf_filter/.config.vsh.yaml

@@ -44,6 +44,9 @@ resources:
 - type: "python_script"
   path: "script.py"
   is_executable: true
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
 description: "Filters a GTF file based on sequence names in a FASTA file.\n"
 test_resources:
 - type: "bash_script"
@@ -135,6 +138,8 @@ runners:
       cpu200: "cpus = 200"
       cpu500: "cpus = 500"
       cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
   debug: false
   container: "docker"
 engines:
@@ -155,8 +160,8 @@ build_info:
   output: "target/nextflow/gtf_filter"
   executable: "target/nextflow/gtf_filter/main.nf"
   viash_version: "0.9.0"
-  git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
-  git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+  git_commit: "4adb388c7d928eea02bccf890214f3b932b08714"
+  git_remote: "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"
@@ -177,8 +182,10 @@ package_config:
   source: "src"
   target: "target"
   config_mods:
-  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
-    \ := '$id'\n"
+  - ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config',\
+    \ dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag\
+    \ := '$id'\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/gtf_filter/main.nf

@@ -2862,6 +2862,11 @@ meta = [
       "type" : "python_script",
       "path" : "script.py",
       "is_executable" : true
+    },
+    {
+      "type" : "file",
+      "path" : "/src/workflows/utils/labels.config",
+      "dest" : "nextflow_labels.config"
     }
   ],
   "description" : "Filters a GTF file based on sequence names in a FASTA file.\n",
@@ -2977,7 +2982,10 @@ meta = [
           "cpu200" : "cpus = 200",
           "cpu500" : "cpus = 500",
           "cpu1000" : "cpus = 1000"
-        }
+        },
+        "script" : [
+          "includeConfig(\\"nextflow_labels.config\\")"
+        ]
       },
       "debug" : false,
       "container" : "docker"
@@ -3003,8 +3011,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/gtf_filter",
     "viash_version" : "0.9.0",
-    "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e",
-    "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+    "git_commit" : "4adb388c7d928eea02bccf890214f3b932b08714",
+    "git_remote" : "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",
@@ -3035,7 +3043,7 @@ meta = [
     "source" : "/workdir/root/repo/src",
     "target" : "/workdir/root/repo/target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
+      ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag := '$id'\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/gtf_filter/nextflow.config

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

target/nextflow/gtf_filter/nextflow_labels.config

@@ -0,0 +1,44 @@
+process {
+  // Default resources for components that hardly do any processing
+  memory = { 2.GB * task.attempt }
+  cpus = 1
+
+  // Retry for exit codes that have something to do with memory issues
+  errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
+  maxRetries = 3
+  maxMemory = null
+
+  // Resource labels
+  withLabel: singlecpu { cpus = 1 }
+  withLabel: lowcpu { cpus = 2 }
+  withLabel: midcpu { cpus = 4 }
+  withLabel: highcpu { cpus = 8 }
+  withLabel: veryhighcpu { cpus = 16 }
+ 
+  withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 24.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 48.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/gunzip/.config.vsh.yaml

@@ -29,6 +29,9 @@ resources:
 - type: "bash_script"
   path: "script.sh"
   is_executable: true
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
 description: "Compress or uncompress a file or list of files.\n"
 test_resources:
 - type: "bash_script"
@@ -119,6 +122,8 @@ runners:
       cpu200: "cpus = 200"
       cpu500: "cpus = 500"
       cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
   debug: false
   container: "docker"
 engines:
@@ -144,8 +149,8 @@ build_info:
   output: "target/nextflow/gunzip"
   executable: "target/nextflow/gunzip/main.nf"
   viash_version: "0.9.0"
-  git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
-  git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+  git_commit: "4adb388c7d928eea02bccf890214f3b932b08714"
+  git_remote: "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"
@@ -166,8 +171,10 @@ package_config:
   source: "src"
   target: "target"
   config_mods:
-  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
-    \ := '$id'\n"
+  - ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config',\
+    \ dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag\
+    \ := '$id'\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/gunzip/main.nf

@@ -2845,6 +2845,11 @@ meta = [
       "type" : "bash_script",
       "path" : "script.sh",
       "is_executable" : true
+    },
+    {
+      "type" : "file",
+      "path" : "/src/workflows/utils/labels.config",
+      "dest" : "nextflow_labels.config"
     }
   ],
   "description" : "Compress or uncompress a file or list of files.\n",
@@ -2957,7 +2962,10 @@ meta = [
           "cpu200" : "cpus = 200",
           "cpu500" : "cpus = 500",
           "cpu1000" : "cpus = 1000"
-        }
+        },
+        "script" : [
+          "includeConfig(\\"nextflow_labels.config\\")"
+        ]
       },
       "debug" : false,
       "container" : "docker"
@@ -2992,8 +3000,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/gunzip",
     "viash_version" : "0.9.0",
-    "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e",
-    "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+    "git_commit" : "4adb388c7d928eea02bccf890214f3b932b08714",
+    "git_remote" : "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",
@@ -3024,7 +3032,7 @@ meta = [
     "source" : "/workdir/root/repo/src",
     "target" : "/workdir/root/repo/target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
+      ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag := '$id'\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/gunzip/nextflow.config

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

target/nextflow/gunzip/nextflow_labels.config

@@ -0,0 +1,44 @@
+process {
+  // Default resources for components that hardly do any processing
+  memory = { 2.GB * task.attempt }
+  cpus = 1
+
+  // Retry for exit codes that have something to do with memory issues
+  errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
+  maxRetries = 3
+  maxMemory = null
+
+  // Resource labels
+  withLabel: singlecpu { cpus = 1 }
+  withLabel: lowcpu { cpus = 2 }
+  withLabel: midcpu { cpus = 4 }
+  withLabel: highcpu { cpus = 8 }
+  withLabel: veryhighcpu { cpus = 16 }
+ 
+  withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 24.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 48.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/multiqc_custom_biotype/.config.vsh.yaml

@@ -63,6 +63,9 @@ resources:
   is_executable: true
 - type: "file"
   path: "biotypes_header.txt"
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
 description: "Calculate features percentage for biotype counts"
 test_resources:
 - type: "bash_script"
@@ -145,6 +148,8 @@ runners:
       cpu200: "cpus = 200"
       cpu500: "cpus = 500"
       cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
   debug: false
   container: "docker"
 engines:
@@ -165,8 +170,8 @@ build_info:
   output: "target/nextflow/multiqc_custom_biotype"
   executable: "target/nextflow/multiqc_custom_biotype/main.nf"
   viash_version: "0.9.0"
-  git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
-  git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+  git_commit: "4adb388c7d928eea02bccf890214f3b932b08714"
+  git_remote: "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"
@@ -187,8 +192,10 @@ package_config:
   source: "src"
   target: "target"
   config_mods:
-  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
-    \ := '$id'\n"
+  - ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config',\
+    \ dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag\
+    \ := '$id'\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/multiqc_custom_biotype/main.nf

@@ -2888,6 +2888,11 @@ meta = [
     {
       "type" : "file",
       "path" : "biotypes_header.txt"
+    },
+    {
+      "type" : "file",
+      "path" : "/src/workflows/utils/labels.config",
+      "dest" : "nextflow_labels.config"
     }
   ],
   "description" : "Calculate features percentage for biotype counts",
@@ -2986,7 +2991,10 @@ meta = [
           "cpu200" : "cpus = 200",
           "cpu500" : "cpus = 500",
           "cpu1000" : "cpus = 1000"
-        }
+        },
+        "script" : [
+          "includeConfig(\\"nextflow_labels.config\\")"
+        ]
       },
       "debug" : false,
       "container" : "docker"
@@ -3012,8 +3020,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/multiqc_custom_biotype",
     "viash_version" : "0.9.0",
-    "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e",
-    "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+    "git_commit" : "4adb388c7d928eea02bccf890214f3b932b08714",
+    "git_remote" : "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",
@@ -3044,7 +3052,7 @@ meta = [
     "source" : "/workdir/root/repo/src",
     "target" : "/workdir/root/repo/target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
+      ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag := '$id'\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/multiqc_custom_biotype/nextflow.config

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

target/nextflow/multiqc_custom_biotype/nextflow_labels.config

@@ -0,0 +1,44 @@
+process {
+  // Default resources for components that hardly do any processing
+  memory = { 2.GB * task.attempt }
+  cpus = 1
+
+  // Retry for exit codes that have something to do with memory issues
+  errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
+  maxRetries = 3
+  maxMemory = null
+
+  // Resource labels
+  withLabel: singlecpu { cpus = 1 }
+  withLabel: lowcpu { cpus = 2 }
+  withLabel: midcpu { cpus = 4 }
+  withLabel: highcpu { cpus = 8 }
+  withLabel: veryhighcpu { cpus = 16 }
+ 
+  withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 24.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 48.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/picard_markduplicates/.config.vsh.yaml

@@ -87,6 +87,9 @@ resources:
 - type: "bash_script"
   path: "script.sh"
   is_executable: true
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
 description: "Locate and tag duplicate reads in a BAM file\n"
 test_resources:
 - type: "bash_script"
@@ -179,6 +182,8 @@ runners:
       cpu200: "cpus = 200"
       cpu500: "cpus = 500"
       cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
   debug: false
   container: "docker"
 engines:
@@ -207,8 +212,8 @@ build_info:
   output: "target/nextflow/picard_markduplicates"
   executable: "target/nextflow/picard_markduplicates/main.nf"
   viash_version: "0.9.0"
-  git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
-  git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+  git_commit: "4adb388c7d928eea02bccf890214f3b932b08714"
+  git_remote: "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"
@@ -229,8 +234,10 @@ package_config:
   source: "src"
   target: "target"
   config_mods:
-  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
-    \ := '$id'\n"
+  - ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config',\
+    \ dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag\
+    \ := '$id'\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/picard_markduplicates/main.nf

@@ -2910,6 +2910,11 @@ meta = [
       "type" : "bash_script",
       "path" : "script.sh",
       "is_executable" : true
+    },
+    {
+      "type" : "file",
+      "path" : "/src/workflows/utils/labels.config",
+      "dest" : "nextflow_labels.config"
     }
   ],
   "description" : "Locate and tag duplicate reads in a BAM file\n",
@@ -3026,7 +3031,10 @@ meta = [
           "cpu200" : "cpus = 200",
           "cpu500" : "cpus = 500",
           "cpu1000" : "cpus = 1000"
-        }
+        },
+        "script" : [
+          "includeConfig(\\"nextflow_labels.config\\")"
+        ]
       },
       "debug" : false,
       "container" : "docker"
@@ -3063,8 +3071,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/picard_markduplicates",
     "viash_version" : "0.9.0",
-    "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e",
-    "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+    "git_commit" : "4adb388c7d928eea02bccf890214f3b932b08714",
+    "git_remote" : "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",
@@ -3095,7 +3103,7 @@ meta = [
     "source" : "/workdir/root/repo/src",
     "target" : "/workdir/root/repo/target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
+      ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag := '$id'\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/picard_markduplicates/nextflow.config

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

target/nextflow/picard_markduplicates/nextflow_labels.config

@@ -0,0 +1,44 @@
+process {
+  // Default resources for components that hardly do any processing
+  memory = { 2.GB * task.attempt }
+  cpus = 1
+
+  // Retry for exit codes that have something to do with memory issues
+  errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
+  maxRetries = 3
+  maxMemory = null
+
+  // Resource labels
+  withLabel: singlecpu { cpus = 1 }
+  withLabel: lowcpu { cpus = 2 }
+  withLabel: midcpu { cpus = 4 }
+  withLabel: highcpu { cpus = 8 }
+  withLabel: veryhighcpu { cpus = 16 }
+ 
+  withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 24.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 48.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/prepare_multiqc_input/.config.vsh.yaml

@@ -287,6 +287,7 @@ argument_groups:
     multiple_sep: ","
   - type: "file"
     name: "--multiqc_config"
+    description: "Custom multiqc configuration file\n"
     info: null
     must_exist: true
     create_parent: true
@@ -311,6 +312,11 @@ resources:
 - type: "bash_script"
   path: "script.sh"
   is_executable: true
+- type: "file"
+  path: "multiqc_config.yml"
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
 description: "Prepare directory with all the input files for MultiQC.\n"
 info: null
 status: "enabled"
@@ -389,6 +395,8 @@ runners:
       cpu200: "cpus = 200"
       cpu500: "cpus = 500"
       cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
   debug: false
   container: "docker"
 engines:
@@ -409,8 +417,8 @@ build_info:
   output: "target/nextflow/prepare_multiqc_input"
   executable: "target/nextflow/prepare_multiqc_input/main.nf"
   viash_version: "0.9.0"
-  git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
-  git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+  git_commit: "4adb388c7d928eea02bccf890214f3b932b08714"
+  git_remote: "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"
@@ -431,8 +439,10 @@ package_config:
   source: "src"
   target: "target"
   config_mods:
-  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
-    \ := '$id'\n"
+  - ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config',\
+    \ dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag\
+    \ := '$id'\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/prepare_multiqc_input/main.nf

@@ -3127,6 +3127,7 @@ meta = [
         {
           "type" : "file",
           "name" : "--multiqc_config",
+          "description" : "Custom multiqc configuration file\n",
           "must_exist" : true,
           "create_parent" : true,
           "required" : false,
@@ -3160,6 +3161,15 @@ meta = [
       "type" : "bash_script",
       "path" : "script.sh",
       "is_executable" : true
+    },
+    {
+      "type" : "file",
+      "path" : "/src/assets/multiqc_config.yml"
+    },
+    {
+      "type" : "file",
+      "path" : "/src/workflows/utils/labels.config",
+      "dest" : "nextflow_labels.config"
     }
   ],
   "description" : "Prepare directory with all the input files for MultiQC.\n",
@@ -3251,7 +3261,10 @@ meta = [
           "cpu200" : "cpus = 200",
           "cpu500" : "cpus = 500",
           "cpu1000" : "cpus = 1000"
-        }
+        },
+        "script" : [
+          "includeConfig(\\"nextflow_labels.config\\")"
+        ]
       },
       "debug" : false,
       "container" : "docker"
@@ -3277,8 +3290,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/prepare_multiqc_input",
     "viash_version" : "0.9.0",
-    "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e",
-    "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+    "git_commit" : "4adb388c7d928eea02bccf890214f3b932b08714",
+    "git_remote" : "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",
@@ -3309,7 +3322,7 @@ meta = [
     "source" : "/workdir/root/repo/src",
     "target" : "/workdir/root/repo/target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
+      ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag := '$id'\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'"
@@ -3456,7 +3469,23 @@ IFS="," read -ra readduplication_multiqc <<< \\$par_readduplication_multiqc && f
 
 IFS="," read -ra tin_multiqc <<< \\$par_tin_multiqc && for file in "\\${tin_multiqc[@]}"; do [ -e "\\$file" ] && cp -r "\\$file" "\\$par_output/"; done
 
-[ -e "\\$par_multiqc_config" ] && cp -r \\$par_multiqc_config "\\$par_output/"
+echo "Checking for custom multiqc_config"
+# If the variable is empty, we use the default one (registered as a resource)
+if [ -z \\$par_multiqc_config ]; then
+  echo "No multiqc_config provided, using the default"
+  cp \\$meta_resources_dir/multiqc_config.yml "\\$par_output"
+else
+  echo "Optional file provided"
+  if [ -f \\$par_multiqc_config ]; then
+    cp \\$par_multiqc_config "\\$par_output"/multiqc_config.yml
+  else
+    # Unreachable: the Viash-generated module checks this
+    echo "Optional file does not exist"
+    exit 1
+  fi
+fi
+
+echo "Done"
 VIASHMAIN
 bash "$tempscript"
 '''

target/nextflow/prepare_multiqc_input/multiqc_config.yml

@@ -0,0 +1,164 @@
+report_comment: >
+  This report has been generated by the <a href="https://github.com/viash-hub/rnaseq" </a>
+  analysis pipeline. 
+report_section_order:
+  "rnaseq-methods-description":
+    order: -1000
+  software_versions:
+    order: -1001
+  "rnaseq.vsh-summary":
+    order: -1002
+
+export_plots: true
+disable_version_detection: true
+
+# Run only these modules
+run_modules:
+  - custom_content
+  - fastqc
+  - cutadapt
+  - fastp
+  - sortmerna
+  - star
+  - rsem
+  - salmon
+  - kallisto
+  - samtools
+  - picard
+  - preseq
+  - rseqc
+  - qualimap
+
+# Order of modules
+top_modules:
+  - "fail_trimming"
+  - "fail_mapping"
+  - "fail_strand"
+  - "star_rsem_deseq2_pca"
+  - "star_rsem_deseq2_clustering"
+  - "star_salmon_deseq2_pca"
+  - "star_salmon_deseq2_clustering"
+  - "salmon_deseq2_pca"
+  - "salmon_deseq2_clustering"
+  - "kallisto_deseq2_pca"
+  - "kallisto_deseq2_clustering"
+  - "biotype_counts"
+  - "dupradar"
+
+module_order:
+  - fastqc:
+      name: "FastQC (raw)"
+      info: "This section of the report shows FastQC results before adapter trimming."
+      path_filters:
+        - "*.read_*.fastqc.zip"
+  - cutadapt
+  - fastp
+  - fastqc:
+      name: "FastQC (trimmed)"
+      info: "This section of the report shows FastQC results after adapter trimming."
+      path_filters:
+        - "*.trimgalore.read_*.fastqc.zip"
+
+# Don't show % Dups in the General Stats table (we have this from Picard)
+table_columns_visible:
+  fastqc:
+    percent_duplicates: False
+
+extra_fn_clean_extn:
+  # - ".mapping_quality"
+  # - ".MarkDuplicates_flagstat.output.flagstat"
+  # - ".MarkDuplicates_idxstats.output.idxstats"
+  # - ".MarkDuplicates_stats.output.txt"
+  # - ".genome_sorted_MarkDuplicates.output.bam"
+  # - ".genome_sorted_MarkDuplicates"
+  - ".read_1"  
+  - ".read_2"  
+
+# See https://github.com/ewels/MultiQC_TestData/blob/master/data/custom_content/with_config/table_headerconfig/multiqc_config.yaml
+custom_data:
+  fail_trimming:
+    section_name: "WARNING: Fail Trimming Check"
+    description: "List of samples that failed the minimum trimmed reads threshold specified via the '--min_trimmed_reads' parameter, and hence were ignored for the downstream processing steps."
+    plot_type: "table"
+    pconfig:
+      id: "fail_trimmed_samples_table"
+      table_title: "Samples failed trimming threshold"
+      namespace: "Samples failed trimming threshold"
+      format: "{:.0f}"
+  fail_mapping:
+    section_name: "WARNING: Fail Alignment Check"
+    description: "List of samples that failed the STAR minimum mapped reads threshold specified via the '--min_mapped_reads' parameter, and hence were ignored for the downstream processing steps."
+    plot_type: "table"
+    pconfig:
+      id: "fail_mapped_samples_table"
+      table_title: "Samples failed mapping threshold"
+      namespace: "Samples failed mapping threshold"
+      format: "{:.2f}"
+  fail_strand:
+    section_name: "WARNING: Fail Strand Check"
+    description: "List of samples that failed the strandedness check between that provided in the samplesheet and calculated by the <a href='http://rseqc.sourceforge.net/#infer-experiment-py'>RSeQC infer_experiment.py</a> tool."
+    plot_type: "table"
+    pconfig:
+      id: "fail_strand_check_table"
+      table_title: "Samples failed strandedness check"
+      namespace: "Samples failed strandedness check"
+      format: "{:.2f}"
+
+# Customise the module search patterns to speed up execution time
+#  - Skip module sub-tools that we are not interested in
+#  - Replace file-content searching with filename pattern searching
+#  - Don't add anything that is the same as the MultiQC default
+# See https://multiqc.info/docs/#optimise-file-search-patterns for details
+sp:
+
+  fastqc/zip:
+    fn: "*.fastqc.zip"
+
+  cutadapt:
+    fn: "*.trimming_report*.txt"
+
+  fastp:
+    fn: "*.fastp_out.json"
+
+  sortmerna:
+    fn: "*sortmerna*.log"
+
+  star:
+    fn: "*.star_align_reads.log.txt"
+
+  # hisat2:
+  #   fn: "*.hisat2.summary.log"
+  # salmon:
+  #   fn: "*meta_info.json"
+
+  preseq:
+    fn: "*.lc_extrap.txt"
+
+  samtools/stats:
+    fn: "*_stats.output.txt"
+  samtools/flagstat:
+    fn: "*_flagstat.output.flagstat"
+  samtools/idxstats:
+    fn: "*_idxstats.output.idxstats"
+
+  rseqc/bam_stat:
+    fn: "*.mapping_quality.txt"
+  rseqc/junction_saturation:
+    fn: "*.junction_saturation_plot.r"
+  rseqc/junction_annotation:
+    fn: "*.junction_annotation.log"
+  rseqc/read_duplication_pos:
+    fn: "*.duplication_rate_mapping.xls"
+  rseqc/read_distribution:
+    fn: "*.read_distribution.txt"
+  rseqc/infer_experiment:
+    fn: "*.strandedness.txt"
+  rseqc/inner_distance:
+    fn: "*.inner_distance_freq.txt"
+  rseqc/tin:
+    fn: "*.tin_summary.txt"
+
+  picard/markdups:
+    fn: "*.MarkDuplicates.metrics.txt"
+
+skip_versions_section: true

target/nextflow/prepare_multiqc_input/nextflow.config

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

target/nextflow/prepare_multiqc_input/nextflow_labels.config

@@ -0,0 +1,44 @@
+process {
+  // Default resources for components that hardly do any processing
+  memory = { 2.GB * task.attempt }
+  cpus = 1
+
+  // Retry for exit codes that have something to do with memory issues
+  errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
+  maxRetries = 3
+  maxMemory = null
+
+  // Resource labels
+  withLabel: singlecpu { cpus = 1 }
+  withLabel: lowcpu { cpus = 2 }
+  withLabel: midcpu { cpus = 4 }
+  withLabel: highcpu { cpus = 8 }
+  withLabel: veryhighcpu { cpus = 16 }
+ 
+  withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 24.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 48.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/prepare_multiqc_input/nextflow_schema.json

@@ -337,8 +337,8 @@
                 "multiqc_config": {
                 "type":
                 "string",
-                "description": "Type: `file`. ",
-                "help_text": "Type: `file`. "
+                "description": "Type: `file`. Custom multiqc configuration file\n",
+                "help_text": "Type: `file`. Custom multiqc configuration file\n"
             
             }
     

target/nextflow/preprocess_transcripts_fasta/.config.vsh.yaml

@@ -29,6 +29,9 @@ resources:
 - type: "bash_script"
   path: "script.sh"
   is_executable: true
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
 description: "Process transcripts FASTA if GTF file is GENOCODE format\n"
 test_resources:
 - type: "bash_script"
@@ -118,6 +121,8 @@ runners:
       cpu200: "cpus = 200"
       cpu500: "cpus = 500"
       cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
   debug: false
   container: "docker"
 engines:
@@ -138,8 +143,8 @@ build_info:
   output: "target/nextflow/preprocess_transcripts_fasta"
   executable: "target/nextflow/preprocess_transcripts_fasta/main.nf"
   viash_version: "0.9.0"
-  git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
-  git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+  git_commit: "4adb388c7d928eea02bccf890214f3b932b08714"
+  git_remote: "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"
@@ -160,8 +165,10 @@ package_config:
   source: "src"
   target: "target"
   config_mods:
-  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
-    \ := '$id'\n"
+  - ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config',\
+    \ dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag\
+    \ := '$id'\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/preprocess_transcripts_fasta/main.nf

@@ -2845,6 +2845,11 @@ meta = [
       "type" : "bash_script",
       "path" : "script.sh",
       "is_executable" : true
+    },
+    {
+      "type" : "file",
+      "path" : "/src/workflows/utils/labels.config",
+      "dest" : "nextflow_labels.config"
     }
   ],
   "description" : "Process transcripts FASTA if GTF file is GENOCODE format\n",
@@ -2956,7 +2961,10 @@ meta = [
           "cpu200" : "cpus = 200",
           "cpu500" : "cpus = 500",
           "cpu1000" : "cpus = 1000"
-        }
+        },
+        "script" : [
+          "includeConfig(\\"nextflow_labels.config\\")"
+        ]
       },
       "debug" : false,
       "container" : "docker"
@@ -2982,8 +2990,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/preprocess_transcripts_fasta",
     "viash_version" : "0.9.0",
-    "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e",
-    "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+    "git_commit" : "4adb388c7d928eea02bccf890214f3b932b08714",
+    "git_remote" : "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",
@@ -3014,7 +3022,7 @@ meta = [
     "source" : "/workdir/root/repo/src",
     "target" : "/workdir/root/repo/target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
+      ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag := '$id'\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/preprocess_transcripts_fasta/nextflow.config

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

target/nextflow/preprocess_transcripts_fasta/nextflow_labels.config

@@ -0,0 +1,44 @@
+process {
+  // Default resources for components that hardly do any processing
+  memory = { 2.GB * task.attempt }
+  cpus = 1
+
+  // Retry for exit codes that have something to do with memory issues
+  errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
+  maxRetries = 3
+  maxMemory = null
+
+  // Resource labels
+  withLabel: singlecpu { cpus = 1 }
+  withLabel: lowcpu { cpus = 2 }
+  withLabel: midcpu { cpus = 4 }
+  withLabel: highcpu { cpus = 8 }
+  withLabel: veryhighcpu { cpus = 16 }
+ 
+  withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 24.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 48.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/preseq_lcextrap/.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: "Computing the expected future yield of distinct reads and bounds on\
   \ the number of total distinct reads in the library and the associated confidence\
   \ intervals."
@@ -139,6 +142,8 @@ runners:
       cpu200: "cpus = 200"
       cpu500: "cpus = 500"
       cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
   debug: false
   container: "docker"
 engines:
@@ -191,8 +196,8 @@ build_info:
   output: "target/nextflow/preseq_lcextrap"
   executable: "target/nextflow/preseq_lcextrap/main.nf"
   viash_version: "0.9.0"
-  git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
-  git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+  git_commit: "4adb388c7d928eea02bccf890214f3b932b08714"
+  git_remote: "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"
@@ -213,8 +218,10 @@ package_config:
   source: "src"
   target: "target"
   config_mods:
-  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
-    \ := '$id'\n"
+  - ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config',\
+    \ dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag\
+    \ := '$id'\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/preseq_lcextrap/main.nf

@@ -2864,6 +2864,11 @@ meta = [
       "type" : "bash_script",
       "path" : "script.sh",
       "is_executable" : true
+    },
+    {
+      "type" : "file",
+      "path" : "/src/workflows/utils/labels.config",
+      "dest" : "nextflow_labels.config"
     }
   ],
   "description" : "Computing the expected future yield of distinct reads and bounds on the number of total distinct reads in the library and the associated confidence intervals.",
@@ -2980,7 +2985,10 @@ meta = [
           "cpu200" : "cpus = 200",
           "cpu500" : "cpus = 500",
           "cpu1000" : "cpus = 1000"
-        }
+        },
+        "script" : [
+          "includeConfig(\\"nextflow_labels.config\\")"
+        ]
       },
       "debug" : false,
       "container" : "docker"
@@ -3035,8 +3043,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/preseq_lcextrap",
     "viash_version" : "0.9.0",
-    "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e",
-    "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+    "git_commit" : "4adb388c7d928eea02bccf890214f3b932b08714",
+    "git_remote" : "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",
@@ -3067,7 +3075,7 @@ meta = [
     "source" : "/workdir/root/repo/src",
     "target" : "/workdir/root/repo/target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
+      ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag := '$id'\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/preseq_lcextrap/nextflow.config

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

target/nextflow/preseq_lcextrap/nextflow_labels.config

@@ -0,0 +1,44 @@
+process {
+  // Default resources for components that hardly do any processing
+  memory = { 2.GB * task.attempt }
+  cpus = 1
+
+  // Retry for exit codes that have something to do with memory issues
+  errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
+  maxRetries = 3
+  maxMemory = null
+
+  // Resource labels
+  withLabel: singlecpu { cpus = 1 }
+  withLabel: lowcpu { cpus = 2 }
+  withLabel: midcpu { cpus = 4 }
+  withLabel: highcpu { cpus = 8 }
+  withLabel: veryhighcpu { cpus = 16 }
+ 
+  withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 24.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 48.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/rsem_merge_counts/.config.vsh.yaml

@@ -77,6 +77,9 @@ resources:
 - type: "bash_script"
   path: "script.sh"
   is_executable: true
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
 description: "Merge the transcript quantification results obtained from rsem calculate-expression\
   \ across all samples.\n"
 info:
@@ -161,6 +164,8 @@ runners:
       cpu200: "cpus = 200"
       cpu500: "cpus = 500"
       cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
   debug: false
   container: "docker"
 engines:
@@ -181,8 +186,8 @@ build_info:
   output: "target/nextflow/rsem_merge_counts"
   executable: "target/nextflow/rsem_merge_counts/main.nf"
   viash_version: "0.9.0"
-  git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
-  git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+  git_commit: "4adb388c7d928eea02bccf890214f3b932b08714"
+  git_remote: "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"
@@ -203,8 +208,10 @@ package_config:
   source: "src"
   target: "target"
   config_mods:
-  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
-    \ := '$id'\n"
+  - ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config',\
+    \ dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag\
+    \ := '$id'\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/rsem_merge_counts/main.nf

@@ -2901,6 +2901,11 @@ meta = [
       "type" : "bash_script",
       "path" : "script.sh",
       "is_executable" : true
+    },
+    {
+      "type" : "file",
+      "path" : "/src/workflows/utils/labels.config",
+      "dest" : "nextflow_labels.config"
     }
   ],
   "description" : "Merge the transcript quantification results obtained from rsem calculate-expression across all samples.\n",
@@ -3001,7 +3006,10 @@ meta = [
           "cpu200" : "cpus = 200",
           "cpu500" : "cpus = 500",
           "cpu1000" : "cpus = 1000"
-        }
+        },
+        "script" : [
+          "includeConfig(\\"nextflow_labels.config\\")"
+        ]
       },
       "debug" : false,
       "container" : "docker"
@@ -3027,8 +3035,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/rsem_merge_counts",
     "viash_version" : "0.9.0",
-    "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e",
-    "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+    "git_commit" : "4adb388c7d928eea02bccf890214f3b932b08714",
+    "git_remote" : "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",
@@ -3059,7 +3067,7 @@ meta = [
     "source" : "/workdir/root/repo/src",
     "target" : "/workdir/root/repo/target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
+      ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag := '$id'\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/rsem_merge_counts/nextflow.config

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

target/nextflow/rsem_merge_counts/nextflow_labels.config

@@ -0,0 +1,44 @@
+process {
+  // Default resources for components that hardly do any processing
+  memory = { 2.GB * task.attempt }
+  cpus = 1
+
+  // Retry for exit codes that have something to do with memory issues
+  errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
+  maxRetries = 3
+  maxMemory = null
+
+  // Resource labels
+  withLabel: singlecpu { cpus = 1 }
+  withLabel: lowcpu { cpus = 2 }
+  withLabel: midcpu { cpus = 4 }
+  withLabel: highcpu { cpus = 8 }
+  withLabel: veryhighcpu { cpus = 16 }
+ 
+  withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 24.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 48.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/rseqc/rseqc_junctionannotation/.config.vsh.yaml

@@ -139,6 +139,9 @@ resources:
 - type: "bash_script"
   path: "script.sh"
   is_executable: true
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
 description: "Compare detected splice junctions to reference gene model.\n"
 test_resources:
 - type: "bash_script"
@@ -229,6 +232,8 @@ runners:
       cpu200: "cpus = 200"
       cpu500: "cpus = 500"
       cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
   debug: false
   container: "docker"
 engines:
@@ -260,8 +265,8 @@ build_info:
   output: "target/nextflow/rseqc/rseqc_junctionannotation"
   executable: "target/nextflow/rseqc/rseqc_junctionannotation/main.nf"
   viash_version: "0.9.0"
-  git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
-  git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+  git_commit: "4adb388c7d928eea02bccf890214f3b932b08714"
+  git_remote: "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"
@@ -282,8 +287,10 @@ package_config:
   source: "src"
   target: "target"
   config_mods:
-  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
-    \ := '$id'\n"
+  - ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config',\
+    \ dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag\
+    \ := '$id'\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/rseqc/rseqc_junctionannotation/main.nf

@@ -2970,6 +2970,11 @@ meta = [
       "type" : "bash_script",
       "path" : "script.sh",
       "is_executable" : true
+    },
+    {
+      "type" : "file",
+      "path" : "/src/workflows/utils/labels.config",
+      "dest" : "nextflow_labels.config"
     }
   ],
   "description" : "Compare detected splice junctions to reference gene model.\n",
@@ -3084,7 +3089,10 @@ meta = [
           "cpu200" : "cpus = 200",
           "cpu500" : "cpus = 500",
           "cpu1000" : "cpus = 1000"
-        }
+        },
+        "script" : [
+          "includeConfig(\\"nextflow_labels.config\\")"
+        ]
       },
       "debug" : false,
       "container" : "docker"
@@ -3128,8 +3136,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_junctionannotation",
     "viash_version" : "0.9.0",
-    "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e",
-    "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+    "git_commit" : "4adb388c7d928eea02bccf890214f3b932b08714",
+    "git_remote" : "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",
@@ -3160,7 +3168,7 @@ meta = [
     "source" : "/workdir/root/repo/src",
     "target" : "/workdir/root/repo/target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
+      ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag := '$id'\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/rseqc/rseqc_junctionannotation/nextflow.config

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

target/nextflow/rseqc/rseqc_junctionannotation/nextflow_labels.config

@@ -0,0 +1,44 @@
+process {
+  // Default resources for components that hardly do any processing
+  memory = { 2.GB * task.attempt }
+  cpus = 1
+
+  // Retry for exit codes that have something to do with memory issues
+  errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
+  maxRetries = 3
+  maxMemory = null
+
+  // Resource labels
+  withLabel: singlecpu { cpus = 1 }
+  withLabel: lowcpu { cpus = 2 }
+  withLabel: midcpu { cpus = 4 }
+  withLabel: highcpu { cpus = 8 }
+  withLabel: veryhighcpu { cpus = 16 }
+ 
+  withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 24.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 48.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/rseqc/rseqc_junctionsaturation/.config.vsh.yaml

@@ -128,6 +128,9 @@ resources:
 - type: "bash_script"
   path: "script.sh"
   is_executable: true
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
 description: "Compare detected splice junctions to reference gene model.\n"
 test_resources:
 - type: "bash_script"
@@ -218,6 +221,8 @@ runners:
       cpu200: "cpus = 200"
       cpu500: "cpus = 500"
       cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
   debug: false
   container: "docker"
 engines:
@@ -249,8 +254,8 @@ build_info:
   output: "target/nextflow/rseqc/rseqc_junctionsaturation"
   executable: "target/nextflow/rseqc/rseqc_junctionsaturation/main.nf"
   viash_version: "0.9.0"
-  git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
-  git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+  git_commit: "4adb388c7d928eea02bccf890214f3b932b08714"
+  git_remote: "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"
@@ -271,8 +276,10 @@ package_config:
   source: "src"
   target: "target"
   config_mods:
-  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
-    \ := '$id'\n"
+  - ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config',\
+    \ dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag\
+    \ := '$id'\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/rseqc/rseqc_junctionsaturation/main.nf

@@ -2955,6 +2955,11 @@ meta = [
       "type" : "bash_script",
       "path" : "script.sh",
       "is_executable" : true
+    },
+    {
+      "type" : "file",
+      "path" : "/src/workflows/utils/labels.config",
+      "dest" : "nextflow_labels.config"
     }
   ],
   "description" : "Compare detected splice junctions to reference gene model.\n",
@@ -3069,7 +3074,10 @@ meta = [
           "cpu200" : "cpus = 200",
           "cpu500" : "cpus = 500",
           "cpu1000" : "cpus = 1000"
-        }
+        },
+        "script" : [
+          "includeConfig(\\"nextflow_labels.config\\")"
+        ]
       },
       "debug" : false,
       "container" : "docker"
@@ -3113,8 +3121,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_junctionsaturation",
     "viash_version" : "0.9.0",
-    "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e",
-    "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+    "git_commit" : "4adb388c7d928eea02bccf890214f3b932b08714",
+    "git_remote" : "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",
@@ -3145,7 +3153,7 @@ meta = [
     "source" : "/workdir/root/repo/src",
     "target" : "/workdir/root/repo/target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
+      ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag := '$id'\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/rseqc/rseqc_junctionsaturation/nextflow.config

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

target/nextflow/rseqc/rseqc_junctionsaturation/nextflow_labels.config

@@ -0,0 +1,44 @@
+process {
+  // Default resources for components that hardly do any processing
+  memory = { 2.GB * task.attempt }
+  cpus = 1
+
+  // Retry for exit codes that have something to do with memory issues
+  errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
+  maxRetries = 3
+  maxMemory = null
+
+  // Resource labels
+  withLabel: singlecpu { cpus = 1 }
+  withLabel: lowcpu { cpus = 2 }
+  withLabel: midcpu { cpus = 4 }
+  withLabel: highcpu { cpus = 8 }
+  withLabel: veryhighcpu { cpus = 16 }
+ 
+  withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 24.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 48.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/rseqc/rseqc_readdistribution/.config.vsh.yaml

@@ -42,6 +42,9 @@ resources:
 - type: "bash_script"
   path: "script.sh"
   is_executable: true
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
 description: "Calculate how mapped reads are distributed over genomic features.\n"
 test_resources:
 - type: "bash_script"
@@ -132,6 +135,8 @@ runners:
       cpu200: "cpus = 200"
       cpu500: "cpus = 500"
       cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
   debug: false
   container: "docker"
 engines:
@@ -162,8 +167,8 @@ build_info:
   output: "target/nextflow/rseqc/rseqc_readdistribution"
   executable: "target/nextflow/rseqc/rseqc_readdistribution/main.nf"
   viash_version: "0.9.0"
-  git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
-  git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+  git_commit: "4adb388c7d928eea02bccf890214f3b932b08714"
+  git_remote: "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"
@@ -184,8 +189,10 @@ package_config:
   source: "src"
   target: "target"
   config_mods:
-  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
-    \ := '$id'\n"
+  - ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config',\
+    \ dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag\
+    \ := '$id'\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/rseqc/rseqc_readdistribution/main.nf

@@ -2860,6 +2860,11 @@ meta = [
       "type" : "bash_script",
       "path" : "script.sh",
       "is_executable" : true
+    },
+    {
+      "type" : "file",
+      "path" : "/src/workflows/utils/labels.config",
+      "dest" : "nextflow_labels.config"
     }
   ],
   "description" : "Calculate how mapped reads are distributed over genomic features.\n",
@@ -2974,7 +2979,10 @@ meta = [
           "cpu200" : "cpus = 200",
           "cpu500" : "cpus = 500",
           "cpu1000" : "cpus = 1000"
-        }
+        },
+        "script" : [
+          "includeConfig(\\"nextflow_labels.config\\")"
+        ]
       },
       "debug" : false,
       "container" : "docker"
@@ -3017,8 +3025,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_readdistribution",
     "viash_version" : "0.9.0",
-    "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e",
-    "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+    "git_commit" : "4adb388c7d928eea02bccf890214f3b932b08714",
+    "git_remote" : "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",
@@ -3049,7 +3057,7 @@ meta = [
     "source" : "/workdir/root/repo/src",
     "target" : "/workdir/root/repo/target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
+      ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag := '$id'\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/rseqc/rseqc_readdistribution/nextflow.config

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

target/nextflow/rseqc/rseqc_readdistribution/nextflow_labels.config

@@ -0,0 +1,44 @@
+process {
+  // Default resources for components that hardly do any processing
+  memory = { 2.GB * task.attempt }
+  cpus = 1
+
+  // Retry for exit codes that have something to do with memory issues
+  errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
+  maxRetries = 3
+  maxMemory = null
+
+  // Resource labels
+  withLabel: singlecpu { cpus = 1 }
+  withLabel: lowcpu { cpus = 2 }
+  withLabel: midcpu { cpus = 4 }
+  withLabel: highcpu { cpus = 8 }
+  withLabel: veryhighcpu { cpus = 16 }
+ 
+  withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 24.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 48.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/rseqc/rseqc_readduplication/.config.vsh.yaml

@@ -92,6 +92,9 @@ resources:
 - type: "bash_script"
   path: "script.sh"
   is_executable: true
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
 description: "Calculate read duplication rate.\n"
 test_resources:
 - type: "bash_script"
@@ -180,6 +183,8 @@ runners:
       cpu200: "cpus = 200"
       cpu500: "cpus = 500"
       cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
   debug: false
   container: "docker"
 engines:
@@ -211,8 +216,8 @@ build_info:
   output: "target/nextflow/rseqc/rseqc_readduplication"
   executable: "target/nextflow/rseqc/rseqc_readduplication/main.nf"
   viash_version: "0.9.0"
-  git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
-  git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+  git_commit: "4adb388c7d928eea02bccf890214f3b932b08714"
+  git_remote: "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"
@@ -233,8 +238,10 @@ package_config:
   source: "src"
   target: "target"
   config_mods:
-  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
-    \ := '$id'\n"
+  - ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config',\
+    \ dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag\
+    \ := '$id'\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/rseqc/rseqc_readduplication/main.nf

@@ -2917,6 +2917,11 @@ meta = [
       "type" : "bash_script",
       "path" : "script.sh",
       "is_executable" : true
+    },
+    {
+      "type" : "file",
+      "path" : "/src/workflows/utils/labels.config",
+      "dest" : "nextflow_labels.config"
     }
   ],
   "description" : "Calculate read duplication rate.\n",
@@ -3027,7 +3032,10 @@ meta = [
           "cpu200" : "cpus = 200",
           "cpu500" : "cpus = 500",
           "cpu1000" : "cpus = 1000"
-        }
+        },
+        "script" : [
+          "includeConfig(\\"nextflow_labels.config\\")"
+        ]
       },
       "debug" : false,
       "container" : "docker"
@@ -3071,8 +3079,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_readduplication",
     "viash_version" : "0.9.0",
-    "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e",
-    "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+    "git_commit" : "4adb388c7d928eea02bccf890214f3b932b08714",
+    "git_remote" : "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",
@@ -3103,7 +3111,7 @@ meta = [
     "source" : "/workdir/root/repo/src",
     "target" : "/workdir/root/repo/target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
+      ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag := '$id'\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/rseqc/rseqc_readduplication/nextflow.config

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

target/nextflow/rseqc/rseqc_readduplication/nextflow_labels.config

@@ -0,0 +1,44 @@
+process {
+  // Default resources for components that hardly do any processing
+  memory = { 2.GB * task.attempt }
+  cpus = 1
+
+  // Retry for exit codes that have something to do with memory issues
+  errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
+  maxRetries = 3
+  maxMemory = null
+
+  // Resource labels
+  withLabel: singlecpu { cpus = 1 }
+  withLabel: lowcpu { cpus = 2 }
+  withLabel: midcpu { cpus = 4 }
+  withLabel: highcpu { cpus = 8 }
+  withLabel: veryhighcpu { cpus = 16 }
+ 
+  withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 24.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 48.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/rseqc/rseqc_tin/.config.vsh.yaml

@@ -94,6 +94,9 @@ resources:
 - type: "bash_script"
   path: "script.sh"
   is_executable: true
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
 description: "Calculte TIN (transcript integrity number) from RNA-seq reads\n"
 test_resources:
 - type: "bash_script"
@@ -186,6 +189,8 @@ runners:
       cpu200: "cpus = 200"
       cpu500: "cpus = 500"
       cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
   debug: false
   container: "docker"
 engines:
@@ -214,8 +219,8 @@ build_info:
   output: "target/nextflow/rseqc/rseqc_tin"
   executable: "target/nextflow/rseqc/rseqc_tin/main.nf"
   viash_version: "0.9.0"
-  git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
-  git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+  git_commit: "4adb388c7d928eea02bccf890214f3b932b08714"
+  git_remote: "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"
@@ -236,8 +241,10 @@ package_config:
   source: "src"
   target: "target"
   config_mods:
-  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
-    \ := '$id'\n"
+  - ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config',\
+    \ dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag\
+    \ := '$id'\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/rseqc/rseqc_tin/main.nf

@@ -2917,6 +2917,11 @@ meta = [
       "type" : "bash_script",
       "path" : "script.sh",
       "is_executable" : true
+    },
+    {
+      "type" : "file",
+      "path" : "/src/workflows/utils/labels.config",
+      "dest" : "nextflow_labels.config"
     }
   ],
   "description" : "Calculte TIN (transcript integrity number) from RNA-seq reads\n",
@@ -3035,7 +3040,10 @@ meta = [
           "cpu200" : "cpus = 200",
           "cpu500" : "cpus = 500",
           "cpu1000" : "cpus = 1000"
-        }
+        },
+        "script" : [
+          "includeConfig(\\"nextflow_labels.config\\")"
+        ]
       },
       "debug" : false,
       "container" : "docker"
@@ -3076,8 +3084,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_tin",
     "viash_version" : "0.9.0",
-    "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e",
-    "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+    "git_commit" : "4adb388c7d928eea02bccf890214f3b932b08714",
+    "git_remote" : "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",
@@ -3108,7 +3116,7 @@ meta = [
     "source" : "/workdir/root/repo/src",
     "target" : "/workdir/root/repo/target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
+      ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag := '$id'\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/rseqc/rseqc_tin/nextflow.config

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

target/nextflow/rseqc/rseqc_tin/nextflow_labels.config

@@ -0,0 +1,44 @@
+process {
+  // Default resources for components that hardly do any processing
+  memory = { 2.GB * task.attempt }
+  cpus = 1
+
+  // Retry for exit codes that have something to do with memory issues
+  errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
+  maxRetries = 3
+  maxMemory = null
+
+  // Resource labels
+  withLabel: singlecpu { cpus = 1 }
+  withLabel: lowcpu { cpus = 2 }
+  withLabel: midcpu { cpus = 4 }
+  withLabel: highcpu { cpus = 8 }
+  withLabel: veryhighcpu { cpus = 16 }
+ 
+  withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 24.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 48.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/sortmerna/.config.vsh.yaml

@@ -74,6 +74,9 @@ resources:
 - type: "bash_script"
   path: "script.sh"
   is_executable: true
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
 description: "Local sequence alignment tool for filtering, mapping and clustering.\
   \ The main application of SortMeRNA is filtering rRNA from metatranscriptomic data.\
   \ SortMeRNA takes as input files of reads (fasta, fastq, fasta.gz, fastq.gz) and\
@@ -172,6 +175,8 @@ runners:
       cpu200: "cpus = 200"
       cpu500: "cpus = 500"
       cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
   debug: false
   container: "docker"
 engines:
@@ -192,8 +197,8 @@ build_info:
   output: "target/nextflow/sortmerna"
   executable: "target/nextflow/sortmerna/main.nf"
   viash_version: "0.9.0"
-  git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
-  git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+  git_commit: "4adb388c7d928eea02bccf890214f3b932b08714"
+  git_remote: "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"
@@ -214,8 +219,10 @@ package_config:
   source: "src"
   target: "target"
   config_mods:
-  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
-    \ := '$id'\n"
+  - ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config',\
+    \ dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag\
+    \ := '$id'\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/sortmerna/main.nf

@@ -2896,6 +2896,11 @@ meta = [
       "type" : "bash_script",
       "path" : "script.sh",
       "is_executable" : true
+    },
+    {
+      "type" : "file",
+      "path" : "/src/workflows/utils/labels.config",
+      "dest" : "nextflow_labels.config"
     }
   ],
   "description" : "Local sequence alignment tool for filtering, mapping and clustering. The main application of SortMeRNA is filtering rRNA from metatranscriptomic data. SortMeRNA takes as input files of reads (fasta, fastq, fasta.gz, fastq.gz) and one or multiple rRNA database file(s), and sorts apart aligned and rejected reads into two files.\n",
@@ -3016,7 +3021,10 @@ meta = [
           "cpu200" : "cpus = 200",
           "cpu500" : "cpus = 500",
           "cpu1000" : "cpus = 1000"
-        }
+        },
+        "script" : [
+          "includeConfig(\\"nextflow_labels.config\\")"
+        ]
       },
       "debug" : false,
       "container" : "docker"
@@ -3042,8 +3050,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/sortmerna",
     "viash_version" : "0.9.0",
-    "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e",
-    "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+    "git_commit" : "4adb388c7d928eea02bccf890214f3b932b08714",
+    "git_remote" : "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",
@@ -3074,7 +3082,7 @@ meta = [
     "source" : "/workdir/root/repo/src",
     "target" : "/workdir/root/repo/target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
+      ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag := '$id'\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/sortmerna/nextflow.config

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

target/nextflow/sortmerna/nextflow_labels.config

@@ -0,0 +1,44 @@
+process {
+  // Default resources for components that hardly do any processing
+  memory = { 2.GB * task.attempt }
+  cpus = 1
+
+  // Retry for exit codes that have something to do with memory issues
+  errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
+  maxRetries = 3
+  maxMemory = null
+
+  // Resource labels
+  withLabel: singlecpu { cpus = 1 }
+  withLabel: lowcpu { cpus = 2 }
+  withLabel: midcpu { cpus = 4 }
+  withLabel: highcpu { cpus = 8 }
+  withLabel: veryhighcpu { cpus = 16 }
+ 
+  withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 24.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 48.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/stringtie/.config.vsh.yaml

@@ -97,6 +97,9 @@ resources:
 - type: "bash_script"
   path: "script.sh"
   is_executable: true
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
 description: "Transcript assembly and quantification for RNA-Seq\n"
 test_resources:
 - type: "bash_script"
@@ -189,6 +192,8 @@ runners:
       cpu200: "cpus = 200"
       cpu500: "cpus = 500"
       cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
   debug: false
   container: "docker"
 engines:
@@ -216,8 +221,8 @@ build_info:
   output: "target/nextflow/stringtie"
   executable: "target/nextflow/stringtie/main.nf"
   viash_version: "0.9.0"
-  git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
-  git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+  git_commit: "4adb388c7d928eea02bccf890214f3b932b08714"
+  git_remote: "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"
@@ -238,8 +243,10 @@ package_config:
   source: "src"
   target: "target"
   config_mods:
-  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
-    \ := '$id'\n"
+  - ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config',\
+    \ dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag\
+    \ := '$id'\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/stringtie/main.nf

@@ -2923,6 +2923,11 @@ meta = [
       "type" : "bash_script",
       "path" : "script.sh",
       "is_executable" : true
+    },
+    {
+      "type" : "file",
+      "path" : "/src/workflows/utils/labels.config",
+      "dest" : "nextflow_labels.config"
     }
   ],
   "description" : "Transcript assembly and quantification for RNA-Seq\n",
@@ -3039,7 +3044,10 @@ meta = [
           "cpu200" : "cpus = 200",
           "cpu500" : "cpus = 500",
           "cpu1000" : "cpus = 1000"
-        }
+        },
+        "script" : [
+          "includeConfig(\\"nextflow_labels.config\\")"
+        ]
       },
       "debug" : false,
       "container" : "docker"
@@ -3073,8 +3081,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/stringtie",
     "viash_version" : "0.9.0",
-    "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e",
-    "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+    "git_commit" : "4adb388c7d928eea02bccf890214f3b932b08714",
+    "git_remote" : "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",
@@ -3105,7 +3113,7 @@ meta = [
     "source" : "/workdir/root/repo/src",
     "target" : "/workdir/root/repo/target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
+      ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag := '$id'\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/stringtie/nextflow.config

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

target/nextflow/stringtie/nextflow_labels.config

@@ -0,0 +1,44 @@
+process {
+  // Default resources for components that hardly do any processing
+  memory = { 2.GB * task.attempt }
+  cpus = 1
+
+  // Retry for exit codes that have something to do with memory issues
+  errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
+  maxRetries = 3
+  maxMemory = null
+
+  // Resource labels
+  withLabel: singlecpu { cpus = 1 }
+  withLabel: lowcpu { cpus = 2 }
+  withLabel: midcpu { cpus = 4 }
+  withLabel: highcpu { cpus = 8 }
+  withLabel: veryhighcpu { cpus = 16 }
+ 
+  withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 24.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 48.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/summarizedexperiment/.config.vsh.yaml

@@ -85,6 +85,9 @@ resources:
   is_executable: true
 - type: "file"
   path: "summarizedexperiment.r"
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
 description: "Create SummarizedExperiment object from Salmon counts"
 info:
   migration_info:
@@ -168,6 +171,8 @@ runners:
       cpu200: "cpus = 200"
       cpu500: "cpus = 500"
       cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
   debug: false
   container: "docker"
 engines:
@@ -199,8 +204,8 @@ build_info:
   output: "target/nextflow/summarizedexperiment"
   executable: "target/nextflow/summarizedexperiment/main.nf"
   viash_version: "0.9.0"
-  git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
-  git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+  git_commit: "4adb388c7d928eea02bccf890214f3b932b08714"
+  git_remote: "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"
@@ -221,8 +226,10 @@ package_config:
   source: "src"
   target: "target"
   config_mods:
-  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
-    \ := '$id'\n"
+  - ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config',\
+    \ dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag\
+    \ := '$id'\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/summarizedexperiment/main.nf

@@ -2910,6 +2910,11 @@ meta = [
     {
       "type" : "file",
       "path" : "summarizedexperiment.r"
+    },
+    {
+      "type" : "file",
+      "path" : "/src/workflows/utils/labels.config",
+      "dest" : "nextflow_labels.config"
     }
   ],
   "description" : "Create SummarizedExperiment object from Salmon counts",
@@ -3010,7 +3015,10 @@ meta = [
           "cpu200" : "cpus = 200",
           "cpu500" : "cpus = 500",
           "cpu1000" : "cpus = 1000"
-        }
+        },
+        "script" : [
+          "includeConfig(\\"nextflow_labels.config\\")"
+        ]
       },
       "debug" : false,
       "container" : "docker"
@@ -3054,8 +3062,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/summarizedexperiment",
     "viash_version" : "0.9.0",
-    "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e",
-    "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+    "git_commit" : "4adb388c7d928eea02bccf890214f3b932b08714",
+    "git_remote" : "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",
@@ -3086,7 +3094,7 @@ meta = [
     "source" : "/workdir/root/repo/src",
     "target" : "/workdir/root/repo/target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
+      ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag := '$id'\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/summarizedexperiment/nextflow.config

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

target/nextflow/summarizedexperiment/nextflow_labels.config

@@ -0,0 +1,44 @@
+process {
+  // Default resources for components that hardly do any processing
+  memory = { 2.GB * task.attempt }
+  cpus = 1
+
+  // Retry for exit codes that have something to do with memory issues
+  errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
+  maxRetries = 3
+  maxMemory = null
+
+  // Resource labels
+  withLabel: singlecpu { cpus = 1 }
+  withLabel: lowcpu { cpus = 2 }
+  withLabel: midcpu { cpus = 4 }
+  withLabel: highcpu { cpus = 8 }
+  withLabel: veryhighcpu { cpus = 16 }
+ 
+  withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 24.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 48.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/tx2gene/.config.vsh.yaml

@@ -69,6 +69,9 @@ resources:
   is_executable: true
 - type: "file"
   path: "tx2gene.py"
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
 description: "Get transcript id (tx) to gene names for tximport"
 test_resources:
 - type: "bash_script"
@@ -156,6 +159,8 @@ runners:
       cpu200: "cpus = 200"
       cpu500: "cpus = 500"
       cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
   debug: false
   container: "docker"
 engines:
@@ -185,8 +190,8 @@ build_info:
   output: "target/nextflow/tx2gene"
   executable: "target/nextflow/tx2gene/main.nf"
   viash_version: "0.9.0"
-  git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
-  git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+  git_commit: "4adb388c7d928eea02bccf890214f3b932b08714"
+  git_remote: "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"
@@ -207,8 +212,10 @@ package_config:
   source: "src"
   target: "target"
   config_mods:
-  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
-    \ := '$id'\n"
+  - ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config',\
+    \ dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag\
+    \ := '$id'\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/tx2gene/main.nf

@@ -2895,6 +2895,11 @@ meta = [
     {
       "type" : "file",
       "path" : "tx2gene.py"
+    },
+    {
+      "type" : "file",
+      "path" : "/src/workflows/utils/labels.config",
+      "dest" : "nextflow_labels.config"
     }
   ],
   "description" : "Get transcript id (tx) to gene names for tximport",
@@ -3002,7 +3007,10 @@ meta = [
           "cpu200" : "cpus = 200",
           "cpu500" : "cpus = 500",
           "cpu1000" : "cpus = 1000"
-        }
+        },
+        "script" : [
+          "includeConfig(\\"nextflow_labels.config\\")"
+        ]
       },
       "debug" : false,
       "container" : "docker"
@@ -3043,8 +3051,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/tx2gene",
     "viash_version" : "0.9.0",
-    "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e",
-    "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+    "git_commit" : "4adb388c7d928eea02bccf890214f3b932b08714",
+    "git_remote" : "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",
@@ -3075,7 +3083,7 @@ meta = [
     "source" : "/workdir/root/repo/src",
     "target" : "/workdir/root/repo/target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
+      ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag := '$id'\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/tx2gene/nextflow.config

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

target/nextflow/tx2gene/nextflow_labels.config

@@ -0,0 +1,44 @@
+process {
+  // Default resources for components that hardly do any processing
+  memory = { 2.GB * task.attempt }
+  cpus = 1
+
+  // Retry for exit codes that have something to do with memory issues
+  errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
+  maxRetries = 3
+  maxMemory = null
+
+  // Resource labels
+  withLabel: singlecpu { cpus = 1 }
+  withLabel: lowcpu { cpus = 2 }
+  withLabel: midcpu { cpus = 4 }
+  withLabel: highcpu { cpus = 8 }
+  withLabel: veryhighcpu { cpus = 16 }
+ 
+  withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 24.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 48.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/tximport/.config.vsh.yaml

@@ -128,6 +128,9 @@ resources:
   is_executable: true
 - type: "file"
   path: "tximport.r"
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
 description: "Get dataframe linking transcript ID, gene ID, and gene name"
 test_resources:
 - type: "bash_script"
@@ -215,6 +218,8 @@ runners:
       cpu200: "cpus = 200"
       cpu500: "cpus = 500"
       cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
   debug: false
   container: "docker"
 engines:
@@ -251,8 +256,8 @@ build_info:
   output: "target/nextflow/tximport"
   executable: "target/nextflow/tximport/main.nf"
   viash_version: "0.9.0"
-  git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
-  git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+  git_commit: "4adb388c7d928eea02bccf890214f3b932b08714"
+  git_remote: "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"
@@ -273,8 +278,10 @@ package_config:
   source: "src"
   target: "target"
   config_mods:
-  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
-    \ := '$id'\n"
+  - ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config',\
+    \ dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag\
+    \ := '$id'\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/tximport/main.nf

@@ -2964,6 +2964,11 @@ meta = [
     {
       "type" : "file",
       "path" : "tximport.r"
+    },
+    {
+      "type" : "file",
+      "path" : "/src/workflows/utils/labels.config",
+      "dest" : "nextflow_labels.config"
     }
   ],
   "description" : "Get dataframe linking transcript ID, gene ID, and gene name",
@@ -3071,7 +3076,10 @@ meta = [
           "cpu200" : "cpus = 200",
           "cpu500" : "cpus = 500",
           "cpu1000" : "cpus = 1000"
-        }
+        },
+        "script" : [
+          "includeConfig(\\"nextflow_labels.config\\")"
+        ]
       },
       "debug" : false,
       "container" : "docker"
@@ -3121,8 +3129,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/tximport",
     "viash_version" : "0.9.0",
-    "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e",
-    "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
+    "git_commit" : "4adb388c7d928eea02bccf890214f3b932b08714",
+    "git_remote" : "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",
@@ -3153,7 +3161,7 @@ meta = [
     "source" : "/workdir/root/repo/src",
     "target" : "/workdir/root/repo/target",
     "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
+      ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag := '$id'\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'"