Build branch main_pipeline with version main_pipeline (c918fed)

Build pipeline: viash-hub.htrnaseq.main-pipeline-tgkd9 Source commit: c918fed99a Source message: Merge branch 'main' into main_pipeline
2024-08-20 15:49:37 +00:00
parent 15cd1e1fa3
commit 366c369df1
33 changed files with 609 additions and 63 deletions
--- a/README.md
+++ b/README.md
@@ -1,10 +1,98 @@
-# Viash-enabled HT-RNAseq pipeline
+# HT-RNAseq - A pipeline for processing high-throughput RNA-seq data

 ## Introduction
 __TODO__: Add a description of the pipeline here.

 ## Test data

+As test data, we use [a DRUGseq dataset](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE176150) from the [NCBI Sequence Read Archive](https://www.ncbi.nlm.nih.gov/sra).
+
+The original data has been (partly) subsampled to reduce the test runtime. We used [seqtk](https://github.com/lh3/seqtk) for this with a seed of 1, e.g.:
+
+```bash
+seqtk sample -s1 orig/SRR14730302/VH02001614_S8_R1_001.fastq.gz 10000 > 10k/SRR14730302/VH02001614_S8_R1_001.fastq.gz
+```
+
+The data is available at: `gs://viash-hub-test-data/htrnaseq/v1/`:
+
+```
+❯ gcstree -f viash-hub-test-data/htrnaseq/v1/
+viash-hub-test-data
+└── htrnaseq
+    └── v1
+        ├── [  48]  2-wells.fasta
+        ├── [465.3K]  GSE176150_metadata.csv
+        ├── 100k
+        │   ├── SRR14730301
+        │   │   ├── [8.5M]  VH02001612_S9_R1_001.fastq
+        │   │   └── [14.9M]  VH02001612_S9_R2_001.fastq
+        │   └── SRR14730302
+        │       ├── [8.5M]  VH02001614_S8_R1_001.fastq.gz
+        │       └── [14.9M]  VH02001614_S8_R2_001.fastq.gz
+        ├── 10k
+        │   ├── SRR14730301
+        │   │   ├── [845.4K]  VH02001612_S9_R1_001.fastq
+        │   │   └── [1.5M]  VH02001612_S9_R2_001.fastq
+        │   └── SRR14730302
+        │       ├── [845.3K]  VH02001614_S8_R1_001.fastq.gz
+        │       └── [1.5M]  VH02001614_S8_R2_001.fastq.gz
+        └── orig
+            ├── [20.4G]  SRR14730301
+            │   └── [20.4G]  SRR14730301
+            ├── SRR14730301
+            │   ├── [9.1G]  VH02001612_S9_R1_001.fastq.gz
+            │   └── [22.0G]  VH02001612_S9_R2_001.fastq.gz
+            ├── [16.9G]  SRR14730302
+            │   └── [16.9G]  SRR14730302
+            ├── SRR14730302
+            │   ├── [7.6G]  VH02001614_S8_R1_001.fastq.gz
+            │   └── [18.0G]  VH02001614_S8_R2_001.fastq.gz
+            ├── [18.0G]  SRR14730303
+            │   └── [18.0G]  SRR14730303
+            ├── SRR14730303
+            │   ├── [8.1G]  VH02001618_S7_R1_001.fastq.gz
+            │   └── [19.2G]  VH02001618_S7_R2_001.fastq.gz
+            ├── [16.5G]  SRR14730304
+            │   └── [16.5G]  SRR14730304
+            ├── SRR14730304
+            │   ├── [7.5G]  VH02001700_S6_R1_001.fastq.gz
+            │   └── [17.8G]  VH02001700_S6_R2_001.fastq.gz
+            ├── [19.0G]  SRR14730305
+            │   └── [19.0G]  SRR14730305
+            ├── SRR14730305
+            │   ├── [8.4G]  VH02001702_S5_R1_001.fastq.gz
+            │   └── [20.6G]  VH02001702_S5_R2_001.fastq.gz
+            ├── [14.6G]  SRR14730306
+            │   └── [14.6G]  SRR14730306
+            ├── SRR14730306
+            │   ├── [6.6G]  VH02001704_S4_R1_001.fastq.gz
+            │   └── [16.0G]  VH02001704_S4_R2_001.fastq.gz
+            ├── [21.5G]  SRR14730307
+            │   └── [21.5G]  SRR14730307
+            ├── SRR14730307
+            │   ├── [9.6G]  VH02001708_S3_R1_001.fastq.gz
+            │   └── [23.2G]  VH02001708_S3_R2_001.fastq.gz
+            ├── [20.7G]  SRR14730308
+            │   └── [20.7G]  SRR14730308
+            ├── SRR14730308
+            │   ├── [9.3G]  VH02001710_S2_R1_001.fastq.gz
+            │   └── [22.1G]  VH02001710_S2_R2_001.fastq.gz
+            ├── [15.8G]  SRR14730309
+            │   └── [15.8G]  SRR14730309
+            └── SRR14730309
+                ├── [7.2G]  VH02001712_S1_R1_001.fastq.gz
+                └── [16.9G]  VH02001712_S1_R2_001.fastq.gz
+
+18 directories, 37 files
+```
+
+
+The `orig` directory contains the original fastq files. The fastq files are available for 10k and 100k subsamples in the `10k` and `100k` directories, respectively.
+
+The `2-wells.fasta` file contains the barcodes for 2 wells.
+
+## Test run
+
 The pipeline can be run by creating a `params.yaml` file like this:

 ```yaml
--- a/_viash.yaml
+++ b/_viash.yaml
@@ -1,6 +1,6 @@
 name: htrnaseq
 description: |
-  Demultiplexing pipeline [WIP]
+  High-throughput pipeline [WIP]
 license: MIT
 keywords: [bioinformatics, sequence, high-throughput, mapping, counting, pipeline]
 links:
@@ -11,3 +11,5 @@ viash_version: 0.9.0-RC7

 config_mods: |
  .requirements.commands := ['ps']
+  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
+  .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
--- a/target/executable/parallel_map/.config.vsh.yaml
+++ b/target/executable/parallel_map/.config.vsh.yaml
@@ -110,6 +110,9 @@ resources:
 - type: "bash_script"
  path: "script.sh"
  is_executable: true
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
 description: "Map wells in batch, using STAR\nSpliced Transcripts Alignment to a Reference\
  \ (C) Alexander Dobin\nhttps://github.com/alexdobin/STAR\n"
 test_resources:
@@ -187,6 +190,8 @@ runners:
      cpu200: "cpus = 200"
      cpu500: "cpus = 500"
      cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
  debug: false
  container: "docker"
 engines:
@@ -231,18 +236,20 @@ build_info:
  output: "target/executable/parallel_map"
  executable: "target/executable/parallel_map/parallel_map"
  viash_version: "0.9.0-RC6"
-  git_commit: "bdd7091d5b5982b84103a43fece50c608810e0aa"
+  git_commit: "c918fed99aca1cacf3b2c02ca13c2f0af5ecf3bf"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
  version: "main_pipeline"
-  description: "Demultiplexing pipeline [WIP]\n"
+  description: "High-throughput pipeline [WIP]\n"
  info: null
  viash_version: "0.9.0-RC6"
  source: "src"
  target: "target"
  config_mods:
-  - ".requirements.commands := ['ps']\n"
+  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
+    \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
+    \ dest: 'nextflow_labels.config'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
  - ".engines[.type == 'docker'].target_tag := 'main_pipeline'"
--- a/target/executable/parallel_map/nextflow_labels.config
+++ b/target/executable/parallel_map/nextflow_labels.config
@@ -0,0 +1,43 @@
+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 = 4 }
+  withLabel: midcpu { cpus = 10 }
+  withLabel: highcpu { cpus = 20 }
+  
+  withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
+
+}
+
+def get_memory(to_compare) {
+    if (!process.containsKey("maxMemory") || !process.maxMemory) {
+      return to_compare
+    }
+
+    try {
+      if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
+        return process.maxMemory
+      }
+      else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
+        return max_memory as nextflow.util.MemoryUnit
+      }
+      else {
+        return to_compare
+      }  
+    } catch (all) {
+          println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
+          System.exit(1)
+    }
+  }
--- a/target/executable/parallel_map/parallel_map
+++ b/target/executable/parallel_map/parallel_map
@@ -515,9 +515,9 @@ RUN wget -O $STAR_TARGET $STAR_SOURCE && \
  rm $STAR_TARGET && rm -rf /tmp/STAR_$STAR_VERSION

 LABEL org.opencontainers.image.description="Companion container for running component parallel_map"
-LABEL org.opencontainers.image.created="2024-08-20T15:27:42Z"
+LABEL org.opencontainers.image.created="2024-08-20T15:45:18Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="bdd7091d5b5982b84103a43fece50c608810e0aa"
+LABEL org.opencontainers.image.revision="c918fed99aca1cacf3b2c02ca13c2f0af5ecf3bf"
 LABEL org.opencontainers.image.version="main_pipeline"

 VIASHDOCKER
--- a/target/nextflow/parallel_map/.config.vsh.yaml
+++ b/target/nextflow/parallel_map/.config.vsh.yaml
@@ -110,6 +110,9 @@ resources:
 - type: "bash_script"
  path: "script.sh"
  is_executable: true
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
 description: "Map wells in batch, using STAR\nSpliced Transcripts Alignment to a Reference\
  \ (C) Alexander Dobin\nhttps://github.com/alexdobin/STAR\n"
 test_resources:
@@ -187,6 +190,8 @@ runners:
      cpu200: "cpus = 200"
      cpu500: "cpus = 500"
      cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
  debug: false
  container: "docker"
 engines:
@@ -231,18 +236,20 @@ build_info:
  output: "target/nextflow/parallel_map"
  executable: "target/nextflow/parallel_map/main.nf"
  viash_version: "0.9.0-RC6"
-  git_commit: "bdd7091d5b5982b84103a43fece50c608810e0aa"
+  git_commit: "c918fed99aca1cacf3b2c02ca13c2f0af5ecf3bf"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
  version: "main_pipeline"
-  description: "Demultiplexing pipeline [WIP]\n"
+  description: "High-throughput pipeline [WIP]\n"
  info: null
  viash_version: "0.9.0-RC6"
  source: "src"
  target: "target"
  config_mods:
-  - ".requirements.commands := ['ps']\n"
+  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
+    \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
+    \ dest: 'nextflow_labels.config'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
  - ".engines[.type == 'docker'].target_tag := 'main_pipeline'"
--- a/target/nextflow/parallel_map/main.nf
+++ b/target/nextflow/parallel_map/main.nf
@@ -2916,6 +2916,11 @@ meta = [
      "type" : "bash_script",
      "path" : "script.sh",
      "is_executable" : true
+    },
+    {
+      "type" : "file",
+      "path" : "/src/config/labels.config",
+      "dest" : "nextflow_labels.config"
    }
  ],
  "description" : "Map wells in batch, using STAR\nSpliced Transcripts Alignment to a Reference (C) Alexander Dobin\nhttps://github.com/alexdobin/STAR\n",
@@ -3004,7 +3009,10 @@ meta = [
          "cpu200" : "cpus = 200",
          "cpu500" : "cpus = 500",
          "cpu1000" : "cpus = 1000"
-        }
+        },
+        "script" : [
+          "includeConfig(\\"nextflow_labels.config\\")"
+        ]
      },
      "debug" : false,
      "container" : "docker"
@@ -3059,18 +3067,18 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/parallel_map",
    "viash_version" : "0.9.0-RC6",
-    "git_commit" : "bdd7091d5b5982b84103a43fece50c608810e0aa",
+    "git_commit" : "c918fed99aca1cacf3b2c02ca13c2f0af5ecf3bf",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
    "version" : "main_pipeline",
-    "description" : "Demultiplexing pipeline [WIP]\n",
+    "description" : "High-throughput pipeline [WIP]\n",
    "viash_version" : "0.9.0-RC6",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
-      ".requirements.commands := ['ps']\n",
+      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
      ".engines[.type == 'docker'].target_tag := 'main_pipeline'"
--- a/target/nextflow/parallel_map/nextflow.config
+++ b/target/nextflow/parallel_map/nextflow.config
@@ -122,4 +122,4 @@ process{
  withLabel: cpu1000 { cpus = 1000 }
 }

-
+includeConfig("nextflow_labels.config")
--- a/target/nextflow/parallel_map/nextflow_labels.config
+++ b/target/nextflow/parallel_map/nextflow_labels.config
@@ -0,0 +1,43 @@
+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 = 4 }
+  withLabel: midcpu { cpus = 10 }
+  withLabel: highcpu { cpus = 20 }
+  
+  withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
+
+}
+
+def get_memory(to_compare) {
+    if (!process.containsKey("maxMemory") || !process.maxMemory) {
+      return to_compare
+    }
+
+    try {
+      if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
+        return process.maxMemory
+      }
+      else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
+        return max_memory as nextflow.util.MemoryUnit
+      }
+      else {
+        return to_compare
+      }  
+    } catch (all) {
+          println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
+          System.exit(1)
+    }
+  }
--- a/target/nextflow/workflows/htrnaseq/.config.vsh.yaml
+++ b/target/nextflow/workflows/htrnaseq/.config.vsh.yaml
@@ -73,6 +73,9 @@ resources:
  path: "main.nf"
  is_executable: true
  entrypoint: "run_wf"
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
 info: null
 status: "enabled"
 requirements:
@@ -176,6 +179,8 @@ runners:
      cpu200: "cpus = 200"
      cpu500: "cpus = 500"
      cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
  debug: false
  container: "docker"
 engines:
@@ -190,7 +195,7 @@ build_info:
  output: "target/nextflow/workflows/htrnaseq"
  executable: "target/nextflow/workflows/htrnaseq/main.nf"
  viash_version: "0.9.0-RC6"
-  git_commit: "bdd7091d5b5982b84103a43fece50c608810e0aa"
+  git_commit: "c918fed99aca1cacf3b2c02ca13c2f0af5ecf3bf"
  git_remote: "https://github.com/viash-hub/htrnaseq"
  dependencies:
  - "target/nextflow/workflows/well_demultiplex"
@@ -203,13 +208,15 @@ build_info:
 package_config:
  name: "htrnaseq"
  version: "main_pipeline"
-  description: "Demultiplexing pipeline [WIP]\n"
+  description: "High-throughput pipeline [WIP]\n"
  info: null
  viash_version: "0.9.0-RC6"
  source: "src"
  target: "target"
  config_mods:
-  - ".requirements.commands := ['ps']\n"
+  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
+    \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
+    \ dest: 'nextflow_labels.config'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
  - ".engines[.type == 'docker'].target_tag := 'main_pipeline'"
--- a/target/nextflow/workflows/htrnaseq/main.nf
+++ b/target/nextflow/workflows/htrnaseq/main.nf
@@ -2869,6 +2869,11 @@ meta = [
      "path" : "main.nf",
      "is_executable" : true,
      "entrypoint" : "run_wf"
+    },
+    {
+      "type" : "file",
+      "path" : "/src/config/labels.config",
+      "dest" : "nextflow_labels.config"
    }
  ],
  "status" : "enabled",
@@ -3008,7 +3013,10 @@ meta = [
          "cpu200" : "cpus = 200",
          "cpu500" : "cpus = 500",
          "cpu1000" : "cpus = 1000"
-        }
+        },
+        "script" : [
+          "includeConfig(\\"nextflow_labels.config\\")"
+        ]
      },
      "debug" : false,
      "container" : "docker"
@@ -3030,18 +3038,18 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/workflows/htrnaseq",
    "viash_version" : "0.9.0-RC6",
-    "git_commit" : "bdd7091d5b5982b84103a43fece50c608810e0aa",
+    "git_commit" : "c918fed99aca1cacf3b2c02ca13c2f0af5ecf3bf",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
    "version" : "main_pipeline",
-    "description" : "Demultiplexing pipeline [WIP]\n",
+    "description" : "High-throughput pipeline [WIP]\n",
    "viash_version" : "0.9.0-RC6",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
-      ".requirements.commands := ['ps']\n",
+      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
      ".engines[.type == 'docker'].target_tag := 'main_pipeline'"
--- a/target/nextflow/workflows/htrnaseq/nextflow.config
+++ b/target/nextflow/workflows/htrnaseq/nextflow.config
@@ -121,4 +121,4 @@ process{
  withLabel: cpu1000 { cpus = 1000 }
 }

-
+includeConfig("nextflow_labels.config")
--- a/target/nextflow/workflows/htrnaseq/nextflow_labels.config
+++ b/target/nextflow/workflows/htrnaseq/nextflow_labels.config
@@ -0,0 +1,43 @@
+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 = 4 }
+  withLabel: midcpu { cpus = 10 }
+  withLabel: highcpu { cpus = 20 }
+  
+  withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
+
+}
+
+def get_memory(to_compare) {
+    if (!process.containsKey("maxMemory") || !process.maxMemory) {
+      return to_compare
+    }
+
+    try {
+      if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
+        return process.maxMemory
+      }
+      else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
+        return max_memory as nextflow.util.MemoryUnit
+      }
+      else {
+        return to_compare
+      }  
+    } catch (all) {
+          println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
+          System.exit(1)
+    }
+  }
--- a/target/nextflow/workflows/utils/groupLanes/.config.vsh.yaml
+++ b/target/nextflow/workflows/utils/groupLanes/.config.vsh.yaml
@@ -55,6 +55,9 @@ resources:
  path: "main.nf"
  is_executable: true
  entrypoint: "run_wf"
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
 description: "N/A\n"
 info: null
 status: "enabled"
@@ -124,6 +127,8 @@ runners:
      cpu200: "cpus = 200"
      cpu500: "cpus = 500"
      cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
  debug: false
  container: "docker"
 engines:
@@ -136,18 +141,20 @@ build_info:
  output: "target/nextflow/workflows/utils/groupLanes"
  executable: "target/nextflow/workflows/utils/groupLanes/main.nf"
  viash_version: "0.9.0-RC6"
-  git_commit: "bdd7091d5b5982b84103a43fece50c608810e0aa"
+  git_commit: "c918fed99aca1cacf3b2c02ca13c2f0af5ecf3bf"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
  version: "main_pipeline"
-  description: "Demultiplexing pipeline [WIP]\n"
+  description: "High-throughput pipeline [WIP]\n"
  info: null
  viash_version: "0.9.0-RC6"
  source: "src"
  target: "target"
  config_mods:
-  - ".requirements.commands := ['ps']\n"
+  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
+    \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
+    \ dest: 'nextflow_labels.config'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
  - ".engines[.type == 'docker'].target_tag := 'main_pipeline'"
--- a/target/nextflow/workflows/utils/groupLanes/main.nf
+++ b/target/nextflow/workflows/utils/groupLanes/main.nf
@@ -2849,6 +2849,11 @@ meta = [
      "path" : "main.nf",
      "is_executable" : true,
      "entrypoint" : "run_wf"
+    },
+    {
+      "type" : "file",
+      "path" : "/src/config/labels.config",
+      "dest" : "nextflow_labels.config"
    }
  ],
  "description" : "N/A\n",
@@ -2925,7 +2930,10 @@ meta = [
          "cpu200" : "cpus = 200",
          "cpu500" : "cpus = 500",
          "cpu1000" : "cpus = 1000"
-        }
+        },
+        "script" : [
+          "includeConfig(\\"nextflow_labels.config\\")"
+        ]
      },
      "debug" : false,
      "container" : "docker"
@@ -2943,18 +2951,18 @@ meta = [
    "engine" : "native",
    "output" : "target/nextflow/workflows/utils/groupLanes",
    "viash_version" : "0.9.0-RC6",
-    "git_commit" : "bdd7091d5b5982b84103a43fece50c608810e0aa",
+    "git_commit" : "c918fed99aca1cacf3b2c02ca13c2f0af5ecf3bf",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
    "version" : "main_pipeline",
-    "description" : "Demultiplexing pipeline [WIP]\n",
+    "description" : "High-throughput pipeline [WIP]\n",
    "viash_version" : "0.9.0-RC6",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
-      ".requirements.commands := ['ps']\n",
+      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
      ".engines[.type == 'docker'].target_tag := 'main_pipeline'"
--- a/target/nextflow/workflows/utils/groupLanes/nextflow.config
+++ b/target/nextflow/workflows/utils/groupLanes/nextflow.config
@@ -122,4 +122,4 @@ process{
  withLabel: cpu1000 { cpus = 1000 }
 }

-
+includeConfig("nextflow_labels.config")
--- a/target/nextflow/workflows/utils/groupLanes/nextflow_labels.config
+++ b/target/nextflow/workflows/utils/groupLanes/nextflow_labels.config
@@ -0,0 +1,43 @@
+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 = 4 }
+  withLabel: midcpu { cpus = 10 }
+  withLabel: highcpu { cpus = 20 }
+  
+  withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
+
+}
+
+def get_memory(to_compare) {
+    if (!process.containsKey("maxMemory") || !process.maxMemory) {
+      return to_compare
+    }
+
+    try {
+      if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
+        return process.maxMemory
+      }
+      else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
+        return max_memory as nextflow.util.MemoryUnit
+      }
+      else {
+        return to_compare
+      }  
+    } catch (all) {
+          println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
+          System.exit(1)
+    }
+  }
--- a/target/nextflow/workflows/utils/groupPairs/.config.vsh.yaml
+++ b/target/nextflow/workflows/utils/groupPairs/.config.vsh.yaml
@@ -43,6 +43,9 @@ resources:
  path: "main.nf"
  is_executable: true
  entrypoint: "run_wf"
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
 description: "N/A\n"
 info: null
 status: "enabled"
@@ -112,6 +115,8 @@ runners:
      cpu200: "cpus = 200"
      cpu500: "cpus = 500"
      cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
  debug: false
  container: "docker"
 engines:
@@ -124,18 +129,20 @@ build_info:
  output: "target/nextflow/workflows/utils/groupPairs"
  executable: "target/nextflow/workflows/utils/groupPairs/main.nf"
  viash_version: "0.9.0-RC6"
-  git_commit: "bdd7091d5b5982b84103a43fece50c608810e0aa"
+  git_commit: "c918fed99aca1cacf3b2c02ca13c2f0af5ecf3bf"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
  version: "main_pipeline"
-  description: "Demultiplexing pipeline [WIP]\n"
+  description: "High-throughput pipeline [WIP]\n"
  info: null
  viash_version: "0.9.0-RC6"
  source: "src"
  target: "target"
  config_mods:
-  - ".requirements.commands := ['ps']\n"
+  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
+    \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
+    \ dest: 'nextflow_labels.config'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
  - ".engines[.type == 'docker'].target_tag := 'main_pipeline'"
--- a/target/nextflow/workflows/utils/groupPairs/main.nf
+++ b/target/nextflow/workflows/utils/groupPairs/main.nf
@@ -2835,6 +2835,11 @@ meta = [
      "path" : "main.nf",
      "is_executable" : true,
      "entrypoint" : "run_wf"
+    },
+    {
+      "type" : "file",
+      "path" : "/src/config/labels.config",
+      "dest" : "nextflow_labels.config"
    }
  ],
  "description" : "N/A\n",
@@ -2911,7 +2916,10 @@ meta = [
          "cpu200" : "cpus = 200",
          "cpu500" : "cpus = 500",
          "cpu1000" : "cpus = 1000"
-        }
+        },
+        "script" : [
+          "includeConfig(\\"nextflow_labels.config\\")"
+        ]
      },
      "debug" : false,
      "container" : "docker"
@@ -2929,18 +2937,18 @@ meta = [
    "engine" : "native",
    "output" : "target/nextflow/workflows/utils/groupPairs",
    "viash_version" : "0.9.0-RC6",
-    "git_commit" : "bdd7091d5b5982b84103a43fece50c608810e0aa",
+    "git_commit" : "c918fed99aca1cacf3b2c02ca13c2f0af5ecf3bf",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
    "version" : "main_pipeline",
-    "description" : "Demultiplexing pipeline [WIP]\n",
+    "description" : "High-throughput pipeline [WIP]\n",
    "viash_version" : "0.9.0-RC6",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
-      ".requirements.commands := ['ps']\n",
+      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
      ".engines[.type == 'docker'].target_tag := 'main_pipeline'"
--- a/target/nextflow/workflows/utils/groupPairs/nextflow.config
+++ b/target/nextflow/workflows/utils/groupPairs/nextflow.config
@@ -122,4 +122,4 @@ process{
  withLabel: cpu1000 { cpus = 1000 }
 }

-
+includeConfig("nextflow_labels.config")
--- a/target/nextflow/workflows/utils/groupPairs/nextflow_labels.config
+++ b/target/nextflow/workflows/utils/groupPairs/nextflow_labels.config
@@ -0,0 +1,43 @@
+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 = 4 }
+  withLabel: midcpu { cpus = 10 }
+  withLabel: highcpu { cpus = 20 }
+  
+  withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
+
+}
+
+def get_memory(to_compare) {
+    if (!process.containsKey("maxMemory") || !process.maxMemory) {
+      return to_compare
+    }
+
+    try {
+      if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
+        return process.maxMemory
+      }
+      else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
+        return max_memory as nextflow.util.MemoryUnit
+      }
+      else {
+        return to_compare
+      }  
+    } catch (all) {
+          println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
+          System.exit(1)
+    }
+  }
--- a/target/nextflow/workflows/utils/groupWells/.config.vsh.yaml
+++ b/target/nextflow/workflows/utils/groupWells/.config.vsh.yaml
@@ -75,6 +75,9 @@ resources:
  path: "main.nf"
  is_executable: true
  entrypoint: "run_wf"
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
 description: "N/A\n"
 info: null
 status: "enabled"
@@ -144,6 +147,8 @@ runners:
      cpu200: "cpus = 200"
      cpu500: "cpus = 500"
      cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
  debug: false
  container: "docker"
 engines:
@@ -156,18 +161,20 @@ build_info:
  output: "target/nextflow/workflows/utils/groupWells"
  executable: "target/nextflow/workflows/utils/groupWells/main.nf"
  viash_version: "0.9.0-RC6"
-  git_commit: "bdd7091d5b5982b84103a43fece50c608810e0aa"
+  git_commit: "c918fed99aca1cacf3b2c02ca13c2f0af5ecf3bf"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
  version: "main_pipeline"
-  description: "Demultiplexing pipeline [WIP]\n"
+  description: "High-throughput pipeline [WIP]\n"
  info: null
  viash_version: "0.9.0-RC6"
  source: "src"
  target: "target"
  config_mods:
-  - ".requirements.commands := ['ps']\n"
+  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
+    \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
+    \ dest: 'nextflow_labels.config'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
  - ".engines[.type == 'docker'].target_tag := 'main_pipeline'"
--- a/target/nextflow/workflows/utils/groupWells/main.nf
+++ b/target/nextflow/workflows/utils/groupWells/main.nf
@@ -2873,6 +2873,11 @@ meta = [
      "path" : "main.nf",
      "is_executable" : true,
      "entrypoint" : "run_wf"
+    },
+    {
+      "type" : "file",
+      "path" : "/src/config/labels.config",
+      "dest" : "nextflow_labels.config"
    }
  ],
  "description" : "N/A\n",
@@ -2949,7 +2954,10 @@ meta = [
          "cpu200" : "cpus = 200",
          "cpu500" : "cpus = 500",
          "cpu1000" : "cpus = 1000"
-        }
+        },
+        "script" : [
+          "includeConfig(\\"nextflow_labels.config\\")"
+        ]
      },
      "debug" : false,
      "container" : "docker"
@@ -2967,18 +2975,18 @@ meta = [
    "engine" : "native",
    "output" : "target/nextflow/workflows/utils/groupWells",
    "viash_version" : "0.9.0-RC6",
-    "git_commit" : "bdd7091d5b5982b84103a43fece50c608810e0aa",
+    "git_commit" : "c918fed99aca1cacf3b2c02ca13c2f0af5ecf3bf",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
    "version" : "main_pipeline",
-    "description" : "Demultiplexing pipeline [WIP]\n",
+    "description" : "High-throughput pipeline [WIP]\n",
    "viash_version" : "0.9.0-RC6",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
-      ".requirements.commands := ['ps']\n",
+      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
      ".engines[.type == 'docker'].target_tag := 'main_pipeline'"
--- a/target/nextflow/workflows/utils/groupWells/nextflow.config
+++ b/target/nextflow/workflows/utils/groupWells/nextflow.config
@@ -122,4 +122,4 @@ process{
  withLabel: cpu1000 { cpus = 1000 }
 }

-
+includeConfig("nextflow_labels.config")
--- a/target/nextflow/workflows/utils/groupWells/nextflow_labels.config
+++ b/target/nextflow/workflows/utils/groupWells/nextflow_labels.config
@@ -0,0 +1,43 @@
+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 = 4 }
+  withLabel: midcpu { cpus = 10 }
+  withLabel: highcpu { cpus = 20 }
+  
+  withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
+
+}
+
+def get_memory(to_compare) {
+    if (!process.containsKey("maxMemory") || !process.maxMemory) {
+      return to_compare
+    }
+
+    try {
+      if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
+        return process.maxMemory
+      }
+      else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
+        return max_memory as nextflow.util.MemoryUnit
+      }
+      else {
+        return to_compare
+      }  
+    } catch (all) {
+          println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
+          System.exit(1)
+    }
+  }
--- a/target/nextflow/workflows/utils/splitWells/.config.vsh.yaml
+++ b/target/nextflow/workflows/utils/splitWells/.config.vsh.yaml
@@ -61,6 +61,9 @@ resources:
  path: "main.nf"
  is_executable: true
  entrypoint: "run_wf"
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
 description: "N/A\n"
 info: null
 status: "enabled"
@@ -130,6 +133,8 @@ runners:
      cpu200: "cpus = 200"
      cpu500: "cpus = 500"
      cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
  debug: false
  container: "docker"
 engines:
@@ -142,18 +147,20 @@ build_info:
  output: "target/nextflow/workflows/utils/splitWells"
  executable: "target/nextflow/workflows/utils/splitWells/main.nf"
  viash_version: "0.9.0-RC6"
-  git_commit: "bdd7091d5b5982b84103a43fece50c608810e0aa"
+  git_commit: "c918fed99aca1cacf3b2c02ca13c2f0af5ecf3bf"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
  version: "main_pipeline"
-  description: "Demultiplexing pipeline [WIP]\n"
+  description: "High-throughput pipeline [WIP]\n"
  info: null
  viash_version: "0.9.0-RC6"
  source: "src"
  target: "target"
  config_mods:
-  - ".requirements.commands := ['ps']\n"
+  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
+    \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
+    \ dest: 'nextflow_labels.config'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
  - ".engines[.type == 'docker'].target_tag := 'main_pipeline'"
--- a/target/nextflow/workflows/utils/splitWells/main.nf
+++ b/target/nextflow/workflows/utils/splitWells/main.nf
@@ -2856,6 +2856,11 @@ meta = [
      "path" : "main.nf",
      "is_executable" : true,
      "entrypoint" : "run_wf"
+    },
+    {
+      "type" : "file",
+      "path" : "/src/config/labels.config",
+      "dest" : "nextflow_labels.config"
    }
  ],
  "description" : "N/A\n",
@@ -2932,7 +2937,10 @@ meta = [
          "cpu200" : "cpus = 200",
          "cpu500" : "cpus = 500",
          "cpu1000" : "cpus = 1000"
-        }
+        },
+        "script" : [
+          "includeConfig(\\"nextflow_labels.config\\")"
+        ]
      },
      "debug" : false,
      "container" : "docker"
@@ -2950,18 +2958,18 @@ meta = [
    "engine" : "native",
    "output" : "target/nextflow/workflows/utils/splitWells",
    "viash_version" : "0.9.0-RC6",
-    "git_commit" : "bdd7091d5b5982b84103a43fece50c608810e0aa",
+    "git_commit" : "c918fed99aca1cacf3b2c02ca13c2f0af5ecf3bf",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
    "version" : "main_pipeline",
-    "description" : "Demultiplexing pipeline [WIP]\n",
+    "description" : "High-throughput pipeline [WIP]\n",
    "viash_version" : "0.9.0-RC6",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
-      ".requirements.commands := ['ps']\n",
+      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
      ".engines[.type == 'docker'].target_tag := 'main_pipeline'"
--- a/target/nextflow/workflows/utils/splitWells/nextflow.config
+++ b/target/nextflow/workflows/utils/splitWells/nextflow.config
@@ -122,4 +122,4 @@ process{
  withLabel: cpu1000 { cpus = 1000 }
 }

-
+includeConfig("nextflow_labels.config")
--- a/target/nextflow/workflows/utils/splitWells/nextflow_labels.config
+++ b/target/nextflow/workflows/utils/splitWells/nextflow_labels.config
@@ -0,0 +1,43 @@
+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 = 4 }
+  withLabel: midcpu { cpus = 10 }
+  withLabel: highcpu { cpus = 20 }
+  
+  withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
+
+}
+
+def get_memory(to_compare) {
+    if (!process.containsKey("maxMemory") || !process.maxMemory) {
+      return to_compare
+    }
+
+    try {
+      if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
+        return process.maxMemory
+      }
+      else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
+        return max_memory as nextflow.util.MemoryUnit
+      }
+      else {
+        return to_compare
+      }  
+    } catch (all) {
+          println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
+          System.exit(1)
+    }
+  }
--- a/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml
+++ b/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml
@@ -52,6 +52,9 @@ resources:
  path: "main.nf"
  is_executable: true
  entrypoint: "run_wf"
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
 description: "Demultiplexing on well level"
 test_resources:
 - type: "nextflow_script"
@@ -137,6 +140,8 @@ runners:
      cpu200: "cpus = 200"
      cpu500: "cpus = 500"
      cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
  debug: false
  container: "docker"
 engines:
@@ -151,20 +156,22 @@ build_info:
  output: "target/nextflow/workflows/well_demultiplex"
  executable: "target/nextflow/workflows/well_demultiplex/main.nf"
  viash_version: "0.9.0-RC6"
-  git_commit: "bdd7091d5b5982b84103a43fece50c608810e0aa"
+  git_commit: "c918fed99aca1cacf3b2c02ca13c2f0af5ecf3bf"
  git_remote: "https://github.com/viash-hub/htrnaseq"
  dependencies:
  - "target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/cutadapt"
 package_config:
  name: "htrnaseq"
  version: "main_pipeline"
-  description: "Demultiplexing pipeline [WIP]\n"
+  description: "High-throughput pipeline [WIP]\n"
  info: null
  viash_version: "0.9.0-RC6"
  source: "src"
  target: "target"
  config_mods:
-  - ".requirements.commands := ['ps']\n"
+  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
+    \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
+    \ dest: 'nextflow_labels.config'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
  - ".engines[.type == 'docker'].target_tag := 'main_pipeline'"
--- a/target/nextflow/workflows/well_demultiplex/main.nf
+++ b/target/nextflow/workflows/well_demultiplex/main.nf
@@ -2845,6 +2845,11 @@ meta = [
      "path" : "main.nf",
      "is_executable" : true,
      "entrypoint" : "run_wf"
+    },
+    {
+      "type" : "file",
+      "path" : "/src/config/labels.config",
+      "dest" : "nextflow_labels.config"
    }
  ],
  "description" : "Demultiplexing on well level",
@@ -2947,7 +2952,10 @@ meta = [
          "cpu200" : "cpus = 200",
          "cpu500" : "cpus = 500",
          "cpu1000" : "cpus = 1000"
-        }
+        },
+        "script" : [
+          "includeConfig(\\"nextflow_labels.config\\")"
+        ]
      },
      "debug" : false,
      "container" : "docker"
@@ -2969,18 +2977,18 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/workflows/well_demultiplex",
    "viash_version" : "0.9.0-RC6",
-    "git_commit" : "bdd7091d5b5982b84103a43fece50c608810e0aa",
+    "git_commit" : "c918fed99aca1cacf3b2c02ca13c2f0af5ecf3bf",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
    "name" : "htrnaseq",
    "version" : "main_pipeline",
-    "description" : "Demultiplexing pipeline [WIP]\n",
+    "description" : "High-throughput pipeline [WIP]\n",
    "viash_version" : "0.9.0-RC6",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
-      ".requirements.commands := ['ps']\n",
+      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
      ".engines[.type == 'docker'].target_tag := 'main_pipeline'"
--- a/target/nextflow/workflows/well_demultiplex/nextflow.config
+++ b/target/nextflow/workflows/well_demultiplex/nextflow.config
@@ -122,4 +122,4 @@ process{
  withLabel: cpu1000 { cpus = 1000 }
 }

-
+includeConfig("nextflow_labels.config")
--- a/target/nextflow/workflows/well_demultiplex/nextflow_labels.config
+++ b/target/nextflow/workflows/well_demultiplex/nextflow_labels.config
@@ -0,0 +1,43 @@
+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 = 4 }
+  withLabel: midcpu { cpus = 10 }
+  withLabel: highcpu { cpus = 20 }
+  
+  withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 75.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)
+    }
+  }