Build branch demultiplex/v0.6 with version v0.6.3 to demultiplex on branch v0.6 (4590338)

Build pipeline: viash-hub.demultiplex.v0.6.3-fw6tg Source commit: 459033886f Source message: Bump version to v0.6.3
Build branch demultiplex/v0.6 with version v0.6.2 to demultiplex on branch v0.6 (16ba5d4)
2025-11-05 09:02:52 +00:00 · 2025-10-09 09:50:03 +00:00
58 changed files with 183 additions and 148 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,16 @@
+# demultiplex v0.6.3
+
+## Bug fixes
+
+* `runner`: fix resume functionality when used as subworkflow (PR #70).
+
+# demultiplex v0.6.2
+
+## Bug fixes
+
+* `bases2fastq` is configured with more memory than the previously provided 64GB (the release notes specify at least 6GB per thread).
+* More resources for `fastqc` to improve running times.
+
 # demultiplex v0.6.1

 ## Minor changes
--- a/_viash.yaml
+++ b/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.6.1
+version: v0.6.3
 description: |
  Demultiplexing pipeline
 license: MIT
--- a/src/config/labels.config
+++ b/src/config/labels.config
@@ -21,6 +21,7 @@ process {
  withLabel: lowmem { memory = { get_memory( 8.GB * task.attempt ) } }
  withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
  withLabel: highmem { memory = { get_memory( 64.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 128.GB * task.attempt ) } }

 }

--- a/src/demultiplex/main.nf
+++ b/src/demultiplex/main.nf
@@ -74,7 +74,7 @@ workflow run_wf {
      // run bases2fastq
      | bases2fastq.run(
        runIf: {id, state -> state.demultiplexer in ["bases2fastq"]},
-        directives: [label: ["highmem", "midcpu"]],
+        directives: [label: ["veryhighmem", "midcpu"]],
        fromState: { id, state ->
          [
            "analysis_directory": state.input,
@@ -115,7 +115,7 @@ workflow run_wf {

    output_ch = samples_ch 
      | fastqc.run(
-        directives: [label: ["verylowcpu", "lowmem"]],
+        directives: [label: ["lowcpu", "midmem"]],
        fromState: {id, state ->
          def output_base = "$id/qc/fastqc/*"
          [
--- a/src/runner/main.nf
+++ b/src/runner/main.nf
@@ -86,11 +86,16 @@ workflow run_wf {
          ]
        },
        toState: { id, result, state -> [ 
-            "fastq_output": result.output, 
+            // Most of the output is copied from the input state
+            // This allows for resume functionality to work when using any of these outputs
+            // because the restult state contains a unique date in the path.
+            // Only for the sample QC ouput, multiple results are gathered 
+            // so we must use the resulting output directory.
+            "fastq_output": state.output, 
            "prefix": state.prefix,
-            "multiqc_output": result.output_multiqc,
+            "multiqc_output": state.multiqc_output,
            "sample_qc_output": result.output_sample_qc,
-            "demultiplexer_logs": result.output_demultiplexer_logs,
+            "demultiplexer_logs": state.demultiplexer_logs,
          ]
        },
        directives: [
--- a/src/runner/test.nf
+++ b/src/runner/test.nf
@@ -21,7 +21,7 @@ if (!params.publish_dir) {
            println "Failed to delete temp directory: $e"
        }
    }))
-    params.publish_dir = tempDir
+    params.publish_dir = tempDir.toString()
 }
 // The module inherits the parameters defined before the include statement, 
 // therefore any parameters set afterwards will not be used by the module.
--- a/target/executable/io/interop_summary_to_csv/.config.vsh.yaml
+++ b/target/executable/io/interop_summary_to_csv/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "interop_summary_to_csv"
 namespace: "io"
-version: "v0.6.1"
+version: "v0.6.3"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -135,7 +135,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.6.1"
+  target_tag: "v0.6.3"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -160,11 +160,11 @@ build_info:
  output: "target/executable/io/interop_summary_to_csv"
  executable: "target/executable/io/interop_summary_to_csv/interop_summary_to_csv"
  viash_version: "0.9.4"
-  git_commit: "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea"
+  git_commit: "459033886f31de68cf97477867ff26e27ae6d98e"
  git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
  name: "demultiplex"
-  version: "v0.6.1"
+  version: "v0.6.3"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -180,7 +180,7 @@ package_config:
    )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.6.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/executable/io/interop_summary_to_csv/_viash.yaml
+++ b/target/executable/io/interop_summary_to_csv/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.6.1
+version: v0.6.3
 description: |
  Demultiplexing pipeline
 license: MIT
--- a/target/executable/io/interop_summary_to_csv/interop_summary_to_csv
+++ b/target/executable/io/interop_summary_to_csv/interop_summary_to_csv
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# interop_summary_to_csv v0.6.1
+# interop_summary_to_csv v0.6.3
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -454,10 +454,10 @@ tar -C /tmp/ --no-same-owner --no-same-permissions -xvf /tmp/interop.tar.gz && \
 mv /tmp/interop-1.3.1-Linux-GNU/bin/index-summary /tmp/interop-1.3.1-Linux-GNU/bin/summary /usr/local/bin/

 LABEL org.opencontainers.image.description="Companion container for running component io interop_summary_to_csv"
-LABEL org.opencontainers.image.created="2025-10-03T13:21:51Z"
+LABEL org.opencontainers.image.created="2025-11-05T08:18:10Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="edbd04b6b129080fe2fac4d123af9ce7f1ae57ea"
-LABEL org.opencontainers.image.version="v0.6.1"
+LABEL org.opencontainers.image.revision="459033886f31de68cf97477867ff26e27ae6d98e"
+LABEL org.opencontainers.image.version="v0.6.3"

 VIASHDOCKER
  fi
@@ -574,7 +574,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "interop_summary_to_csv v0.6.1"
+  echo "interop_summary_to_csv v0.6.3"
  echo ""
  echo "Input arguments:"
  echo "    --input"
@@ -635,7 +635,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "interop_summary_to_csv v0.6.1"
+            echo "interop_summary_to_csv v0.6.3"
            exit
            ;;
        --input)
@@ -759,7 +759,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/interop_summary_to_csv:v0.6.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/interop_summary_to_csv:v0.6.3'
  fi

  # print dockerfile
--- a/target/executable/io/interop_summary_to_csv/nextflow_labels.config
+++ b/target/executable/io/interop_summary_to_csv/nextflow_labels.config
@@ -21,6 +21,7 @@ process {
  withLabel: lowmem { memory = { get_memory( 8.GB * task.attempt ) } }
  withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
  withLabel: highmem { memory = { get_memory( 64.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 128.GB * task.attempt ) } }

 }

--- a/target/executable/io/publish/.config.vsh.yaml
+++ b/target/executable/io/publish/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "publish"
 namespace: "io"
-version: "v0.6.1"
+version: "v0.6.3"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -204,7 +204,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.6.1"
+  target_tag: "v0.6.3"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -222,11 +222,11 @@ build_info:
  output: "target/executable/io/publish"
  executable: "target/executable/io/publish/publish"
  viash_version: "0.9.4"
-  git_commit: "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea"
+  git_commit: "459033886f31de68cf97477867ff26e27ae6d98e"
  git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
  name: "demultiplex"
-  version: "v0.6.1"
+  version: "v0.6.3"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -242,7 +242,7 @@ package_config:
    )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.6.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/executable/io/publish/_viash.yaml
+++ b/target/executable/io/publish/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.6.1
+version: v0.6.3
 description: |
  Demultiplexing pipeline
 license: MIT
--- a/target/executable/io/publish/nextflow_labels.config
+++ b/target/executable/io/publish/nextflow_labels.config
@@ -21,6 +21,7 @@ process {
  withLabel: lowmem { memory = { get_memory( 8.GB * task.attempt ) } }
  withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
  withLabel: highmem { memory = { get_memory( 64.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 128.GB * task.attempt ) } }

 }

--- a/target/executable/io/publish/publish
+++ b/target/executable/io/publish/publish
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# publish v0.6.1
+# publish v0.6.3
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -450,10 +450,10 @@ RUN apt-get update && \
  rm -rf /var/lib/apt/lists/*

 LABEL org.opencontainers.image.description="Companion container for running component io publish"
-LABEL org.opencontainers.image.created="2025-10-03T13:21:51Z"
+LABEL org.opencontainers.image.created="2025-11-05T08:18:09Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="edbd04b6b129080fe2fac4d123af9ce7f1ae57ea"
-LABEL org.opencontainers.image.version="v0.6.1"
+LABEL org.opencontainers.image.revision="459033886f31de68cf97477867ff26e27ae6d98e"
+LABEL org.opencontainers.image.version="v0.6.3"

 VIASHDOCKER
  fi
@@ -570,7 +570,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "publish v0.6.1"
+  echo "publish v0.6.3"
  echo ""
  echo "Publish the processed results of the run"
  echo ""
@@ -662,7 +662,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "publish v0.6.1"
+            echo "publish v0.6.3"
            exit
            ;;
        --input)
@@ -869,7 +869,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/publish:v0.6.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/publish:v0.6.3'
  fi

  # print dockerfile
--- a/target/executable/io/untar/.config.vsh.yaml
+++ b/target/executable/io/untar/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "untar"
 namespace: "io"
-version: "v0.6.1"
+version: "v0.6.3"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -141,7 +141,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.6.1"
+  target_tag: "v0.6.3"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -159,11 +159,11 @@ build_info:
  output: "target/executable/io/untar"
  executable: "target/executable/io/untar/untar"
  viash_version: "0.9.4"
-  git_commit: "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea"
+  git_commit: "459033886f31de68cf97477867ff26e27ae6d98e"
  git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
  name: "demultiplex"
-  version: "v0.6.1"
+  version: "v0.6.3"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -179,7 +179,7 @@ package_config:
    )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.6.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/executable/io/untar/_viash.yaml
+++ b/target/executable/io/untar/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.6.1
+version: v0.6.3
 description: |
  Demultiplexing pipeline
 license: MIT
--- a/target/executable/io/untar/nextflow_labels.config
+++ b/target/executable/io/untar/nextflow_labels.config
@@ -21,6 +21,7 @@ process {
  withLabel: lowmem { memory = { get_memory( 8.GB * task.attempt ) } }
  withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
  withLabel: highmem { memory = { get_memory( 64.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 128.GB * task.attempt ) } }

 }

--- a/target/executable/io/untar/untar
+++ b/target/executable/io/untar/untar
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# untar v0.6.1
+# untar v0.6.3
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -450,10 +450,10 @@ RUN apt-get update && \
  rm -rf /var/lib/apt/lists/*

 LABEL org.opencontainers.image.description="Companion container for running component io untar"
-LABEL org.opencontainers.image.created="2025-10-03T13:21:52Z"
+LABEL org.opencontainers.image.created="2025-11-05T08:18:10Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="edbd04b6b129080fe2fac4d123af9ce7f1ae57ea"
-LABEL org.opencontainers.image.version="v0.6.1"
+LABEL org.opencontainers.image.revision="459033886f31de68cf97477867ff26e27ae6d98e"
+LABEL org.opencontainers.image.version="v0.6.3"

 VIASHDOCKER
  fi
@@ -570,7 +570,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "untar v0.6.1"
+  echo "untar v0.6.3"
  echo ""
  echo "Unpack a .tar file. When the contents of the .tar file is just a single"
  echo "directory,"
@@ -641,7 +641,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "untar v0.6.1"
+            echo "untar v0.6.3"
            exit
            ;;
        --input)
@@ -771,7 +771,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/untar:v0.6.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/untar:v0.6.3'
  fi

  # print dockerfile
--- a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml
+++ b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "combine_samples"
 namespace: "dataflow"
-version: "v0.6.1"
+version: "v0.6.3"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -168,11 +168,11 @@ build_info:
  output: "target/nextflow/dataflow/combine_samples"
  executable: "target/nextflow/dataflow/combine_samples/main.nf"
  viash_version: "0.9.4"
-  git_commit: "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea"
+  git_commit: "459033886f31de68cf97477867ff26e27ae6d98e"
  git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
  name: "demultiplex"
-  version: "v0.6.1"
+  version: "v0.6.3"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -188,7 +188,7 @@ package_config:
    )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.6.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/dataflow/combine_samples/_viash.yaml
+++ b/target/nextflow/dataflow/combine_samples/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.6.1
+version: v0.6.3
 description: |
  Demultiplexing pipeline
 license: MIT
--- a/target/nextflow/dataflow/combine_samples/main.nf
+++ b/target/nextflow/dataflow/combine_samples/main.nf
@@ -1,4 +1,4 @@
-// combine_samples v0.6.1
+// combine_samples v0.6.3
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3032,7 +3032,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "combine_samples",
  "namespace" : "dataflow",
-  "version" : "v0.6.1",
+  "version" : "v0.6.3",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -3235,12 +3235,12 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/dataflow/combine_samples",
    "viash_version" : "0.9.4",
-    "git_commit" : "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea",
+    "git_commit" : "459033886f31de68cf97477867ff26e27ae6d98e",
    "git_remote" : "https://github.com/viash-hub/demultiplex"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.6.1",
+    "version" : "v0.6.3",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -3257,7 +3257,7 @@ meta = [
      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.6.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
    ],
    "keywords" : [
      "bioinformatics",
--- a/target/nextflow/dataflow/combine_samples/nextflow.config
+++ b/target/nextflow/dataflow/combine_samples/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'dataflow/combine_samples'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.6.1'
+  version = 'v0.6.3'
  description = 'Combine fastq files from across samples into one event with a list of fastq files per orientation.'
 }

--- a/target/nextflow/dataflow/combine_samples/nextflow_labels.config
+++ b/target/nextflow/dataflow/combine_samples/nextflow_labels.config
@@ -21,6 +21,7 @@ process {
  withLabel: lowmem { memory = { get_memory( 8.GB * task.attempt ) } }
  withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
  withLabel: highmem { memory = { get_memory( 64.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 128.GB * task.attempt ) } }

 }

--- a/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml
+++ b/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "gather_fastqs_and_validate"
 namespace: "dataflow"
-version: "v0.6.1"
+version: "v0.6.3"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -159,11 +159,11 @@ build_info:
  output: "target/nextflow/dataflow/gather_fastqs_and_validate"
  executable: "target/nextflow/dataflow/gather_fastqs_and_validate/main.nf"
  viash_version: "0.9.4"
-  git_commit: "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea"
+  git_commit: "459033886f31de68cf97477867ff26e27ae6d98e"
  git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
  name: "demultiplex"
-  version: "v0.6.1"
+  version: "v0.6.3"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -179,7 +179,7 @@ package_config:
    )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.6.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/dataflow/gather_fastqs_and_validate/_viash.yaml
+++ b/target/nextflow/dataflow/gather_fastqs_and_validate/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.6.1
+version: v0.6.3
 description: |
  Demultiplexing pipeline
 license: MIT
--- a/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
+++ b/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
@@ -1,4 +1,4 @@
-// gather_fastqs_and_validate v0.6.1
+// gather_fastqs_and_validate v0.6.3
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3032,7 +3032,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "gather_fastqs_and_validate",
  "namespace" : "dataflow",
-  "version" : "v0.6.1",
+  "version" : "v0.6.3",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -3232,12 +3232,12 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/dataflow/gather_fastqs_and_validate",
    "viash_version" : "0.9.4",
-    "git_commit" : "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea",
+    "git_commit" : "459033886f31de68cf97477867ff26e27ae6d98e",
    "git_remote" : "https://github.com/viash-hub/demultiplex"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.6.1",
+    "version" : "v0.6.3",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -3254,7 +3254,7 @@ meta = [
      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.6.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
    ],
    "keywords" : [
      "bioinformatics",
--- a/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow.config
+++ b/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'dataflow/gather_fastqs_and_validate'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.6.1'
+  version = 'v0.6.3'
  description = 'From a directory containing fastq files, gather the files per sample \nand validate according to the contents of the sample sheet.\n'
 }

--- a/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow_labels.config
+++ b/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow_labels.config
@@ -21,6 +21,7 @@ process {
  withLabel: lowmem { memory = { get_memory( 8.GB * task.attempt ) } }
  withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
  withLabel: highmem { memory = { get_memory( 64.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 128.GB * task.attempt ) } }

 }

--- a/target/nextflow/demultiplex/.config.vsh.yaml
+++ b/target/nextflow/demultiplex/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "demultiplex"
-version: "v0.6.1"
+version: "v0.6.3"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -268,7 +268,7 @@ build_info:
  output: "target/nextflow/demultiplex"
  executable: "target/nextflow/demultiplex/main.nf"
  viash_version: "0.9.4"
-  git_commit: "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea"
+  git_commit: "459033886f31de68cf97477867ff26e27ae6d98e"
  git_remote: "https://github.com/viash-hub/demultiplex"
  dependencies:
  - "target/nextflow/io/untar"
@@ -282,7 +282,7 @@ build_info:
  - "target/nextflow/detect_demultiplexer"
 package_config:
  name: "demultiplex"
-  version: "v0.6.1"
+  version: "v0.6.3"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -298,7 +298,7 @@ package_config:
    )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.6.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/demultiplex/_viash.yaml
+++ b/target/nextflow/demultiplex/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.6.1
+version: v0.6.3
 description: |
  Demultiplexing pipeline
 license: MIT
--- a/target/nextflow/demultiplex/main.nf
+++ b/target/nextflow/demultiplex/main.nf
@@ -1,4 +1,4 @@
-// demultiplex v0.6.1
+// demultiplex v0.6.3
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3031,7 +3031,7 @@ meta = [
  "resources_dir": moduleDir.toRealPath().normalize(),
  "config": processConfig(readJsonBlob('''{
  "name" : "demultiplex",
-  "version" : "v0.6.1",
+  "version" : "v0.6.3",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -3380,12 +3380,12 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/demultiplex",
    "viash_version" : "0.9.4",
-    "git_commit" : "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea",
+    "git_commit" : "459033886f31de68cf97477867ff26e27ae6d98e",
    "git_remote" : "https://github.com/viash-hub/demultiplex"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.6.1",
+    "version" : "v0.6.3",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -3402,7 +3402,7 @@ meta = [
      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.6.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3510,7 +3510,7 @@ workflow run_wf {
      // run bases2fastq
      | bases2fastq.run(
        runIf: {id, state -> state.demultiplexer in ["bases2fastq"]},
-        directives: [label: ["highmem", "midcpu"]],
+        directives: [label: ["veryhighmem", "midcpu"]],
        fromState: { id, state ->
          [
            "analysis_directory": state.input,
@@ -3551,7 +3551,7 @@ workflow run_wf {

    output_ch = samples_ch 
      | fastqc.run(
-        directives: [label: ["verylowcpu", "lowmem"]],
+        directives: [label: ["lowcpu", "midmem"]],
        fromState: {id, state ->
          def output_base = "$id/qc/fastqc/*"
          [
--- a/target/nextflow/demultiplex/nextflow.config
+++ b/target/nextflow/demultiplex/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'demultiplex'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.6.1'
+  version = 'v0.6.3'
  description = 'Demultiplexing of raw sequencing data'
 }

--- a/target/nextflow/demultiplex/nextflow_labels.config
+++ b/target/nextflow/demultiplex/nextflow_labels.config
@@ -21,6 +21,7 @@ process {
  withLabel: lowmem { memory = { get_memory( 8.GB * task.attempt ) } }
  withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
  withLabel: highmem { memory = { get_memory( 64.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 128.GB * task.attempt ) } }

 }

--- a/target/nextflow/detect_demultiplexer/.config.vsh.yaml
+++ b/target/nextflow/detect_demultiplexer/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "detect_demultiplexer"
-version: "v0.6.1"
+version: "v0.6.3"
 argument_groups:
 - name: "Arguments"
  arguments:
@@ -168,11 +168,11 @@ build_info:
  output: "target/nextflow/detect_demultiplexer"
  executable: "target/nextflow/detect_demultiplexer/main.nf"
  viash_version: "0.9.4"
-  git_commit: "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea"
+  git_commit: "459033886f31de68cf97477867ff26e27ae6d98e"
  git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
  name: "demultiplex"
-  version: "v0.6.1"
+  version: "v0.6.3"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -188,7 +188,7 @@ package_config:
    )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.6.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/detect_demultiplexer/_viash.yaml
+++ b/target/nextflow/detect_demultiplexer/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.6.1
+version: v0.6.3
 description: |
  Demultiplexing pipeline
 license: MIT
--- a/target/nextflow/detect_demultiplexer/main.nf
+++ b/target/nextflow/detect_demultiplexer/main.nf
@@ -1,4 +1,4 @@
-// detect_demultiplexer v0.6.1
+// detect_demultiplexer v0.6.3
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3031,7 +3031,7 @@ meta = [
  "resources_dir": moduleDir.toRealPath().normalize(),
  "config": processConfig(readJsonBlob('''{
  "name" : "detect_demultiplexer",
-  "version" : "v0.6.1",
+  "version" : "v0.6.3",
  "argument_groups" : [
    {
      "name" : "Arguments",
@@ -3224,12 +3224,12 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/detect_demultiplexer",
    "viash_version" : "0.9.4",
-    "git_commit" : "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea",
+    "git_commit" : "459033886f31de68cf97477867ff26e27ae6d98e",
    "git_remote" : "https://github.com/viash-hub/demultiplex"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.6.1",
+    "version" : "v0.6.3",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -3246,7 +3246,7 @@ meta = [
      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.6.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
    ],
    "keywords" : [
      "bioinformatics",
--- a/target/nextflow/detect_demultiplexer/nextflow.config
+++ b/target/nextflow/detect_demultiplexer/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'detect_demultiplexer'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.6.1'
+  version = 'v0.6.3'
  description = 'Detects the demultiplexer and accompanying sample information file which can be \nused to generate the fastq files.\n'
 }

--- a/target/nextflow/detect_demultiplexer/nextflow_labels.config
+++ b/target/nextflow/detect_demultiplexer/nextflow_labels.config
@@ -21,6 +21,7 @@ process {
  withLabel: lowmem { memory = { get_memory( 8.GB * task.attempt ) } }
  withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
  withLabel: highmem { memory = { get_memory( 64.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 128.GB * task.attempt ) } }

 }

--- a/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml
+++ b/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "interop_summary_to_csv"
 namespace: "io"
-version: "v0.6.1"
+version: "v0.6.3"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -135,7 +135,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.6.1"
+  target_tag: "v0.6.3"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -160,11 +160,11 @@ build_info:
  output: "target/nextflow/io/interop_summary_to_csv"
  executable: "target/nextflow/io/interop_summary_to_csv/main.nf"
  viash_version: "0.9.4"
-  git_commit: "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea"
+  git_commit: "459033886f31de68cf97477867ff26e27ae6d98e"
  git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
  name: "demultiplex"
-  version: "v0.6.1"
+  version: "v0.6.3"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -180,7 +180,7 @@ package_config:
    )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.6.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/io/interop_summary_to_csv/_viash.yaml
+++ b/target/nextflow/io/interop_summary_to_csv/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.6.1
+version: v0.6.3
 description: |
  Demultiplexing pipeline
 license: MIT
--- a/target/nextflow/io/interop_summary_to_csv/main.nf
+++ b/target/nextflow/io/interop_summary_to_csv/main.nf
@@ -1,4 +1,4 @@
-// interop_summary_to_csv v0.6.1
+// interop_summary_to_csv v0.6.3
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3032,7 +3032,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "interop_summary_to_csv",
  "namespace" : "io",
-  "version" : "v0.6.1",
+  "version" : "v0.6.3",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -3203,7 +3203,7 @@ meta = [
      "id" : "docker",
      "image" : "debian:stable-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.6.1",
+      "target_tag" : "v0.6.3",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3233,12 +3233,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/interop_summary_to_csv",
    "viash_version" : "0.9.4",
-    "git_commit" : "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea",
+    "git_commit" : "459033886f31de68cf97477867ff26e27ae6d98e",
    "git_remote" : "https://github.com/viash-hub/demultiplex"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.6.1",
+    "version" : "v0.6.3",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -3255,7 +3255,7 @@ meta = [
      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.6.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3699,7 +3699,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/demultiplex/io/interop_summary_to_csv",
-    "tag" : "v0.6.1"
+    "tag" : "v0.6.3"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/io/interop_summary_to_csv/nextflow.config
+++ b/target/nextflow/io/interop_summary_to_csv/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'io/interop_summary_to_csv'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.6.1'
+  version = 'v0.6.3'
 }

 process.container = 'nextflow/bash:latest'
--- a/target/nextflow/io/interop_summary_to_csv/nextflow_labels.config
+++ b/target/nextflow/io/interop_summary_to_csv/nextflow_labels.config
@@ -21,6 +21,7 @@ process {
  withLabel: lowmem { memory = { get_memory( 8.GB * task.attempt ) } }
  withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
  withLabel: highmem { memory = { get_memory( 64.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 128.GB * task.attempt ) } }

 }

--- a/target/nextflow/io/publish/.config.vsh.yaml
+++ b/target/nextflow/io/publish/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "publish"
 namespace: "io"
-version: "v0.6.1"
+version: "v0.6.3"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -204,7 +204,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.6.1"
+  target_tag: "v0.6.3"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -222,11 +222,11 @@ build_info:
  output: "target/nextflow/io/publish"
  executable: "target/nextflow/io/publish/main.nf"
  viash_version: "0.9.4"
-  git_commit: "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea"
+  git_commit: "459033886f31de68cf97477867ff26e27ae6d98e"
  git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
  name: "demultiplex"
-  version: "v0.6.1"
+  version: "v0.6.3"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -242,7 +242,7 @@ package_config:
    )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.6.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/io/publish/_viash.yaml
+++ b/target/nextflow/io/publish/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.6.1
+version: v0.6.3
 description: |
  Demultiplexing pipeline
 license: MIT
--- a/target/nextflow/io/publish/main.nf
+++ b/target/nextflow/io/publish/main.nf
@@ -1,4 +1,4 @@
-// publish v0.6.1
+// publish v0.6.3
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3032,7 +3032,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "publish",
  "namespace" : "io",
-  "version" : "v0.6.1",
+  "version" : "v0.6.3",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -3279,7 +3279,7 @@ meta = [
      "id" : "docker",
      "image" : "debian:stable-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.6.1",
+      "target_tag" : "v0.6.3",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3302,12 +3302,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/publish",
    "viash_version" : "0.9.4",
-    "git_commit" : "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea",
+    "git_commit" : "459033886f31de68cf97477867ff26e27ae6d98e",
    "git_remote" : "https://github.com/viash-hub/demultiplex"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.6.1",
+    "version" : "v0.6.3",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -3324,7 +3324,7 @@ meta = [
      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.6.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3799,7 +3799,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/demultiplex/io/publish",
-    "tag" : "v0.6.1"
+    "tag" : "v0.6.3"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/io/publish/nextflow.config
+++ b/target/nextflow/io/publish/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'io/publish'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.6.1'
+  version = 'v0.6.3'
  description = 'Publish the processed results of the run'
 }

--- a/target/nextflow/io/publish/nextflow_labels.config
+++ b/target/nextflow/io/publish/nextflow_labels.config
@@ -21,6 +21,7 @@ process {
  withLabel: lowmem { memory = { get_memory( 8.GB * task.attempt ) } }
  withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
  withLabel: highmem { memory = { get_memory( 64.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 128.GB * task.attempt ) } }

 }

--- a/target/nextflow/io/untar/.config.vsh.yaml
+++ b/target/nextflow/io/untar/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "untar"
 namespace: "io"
-version: "v0.6.1"
+version: "v0.6.3"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -141,7 +141,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.6.1"
+  target_tag: "v0.6.3"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -159,11 +159,11 @@ build_info:
  output: "target/nextflow/io/untar"
  executable: "target/nextflow/io/untar/main.nf"
  viash_version: "0.9.4"
-  git_commit: "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea"
+  git_commit: "459033886f31de68cf97477867ff26e27ae6d98e"
  git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
  name: "demultiplex"
-  version: "v0.6.1"
+  version: "v0.6.3"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -179,7 +179,7 @@ package_config:
    )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.6.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/io/untar/_viash.yaml
+++ b/target/nextflow/io/untar/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.6.1
+version: v0.6.3
 description: |
  Demultiplexing pipeline
 license: MIT
--- a/target/nextflow/io/untar/main.nf
+++ b/target/nextflow/io/untar/main.nf
@@ -1,4 +1,4 @@
-// untar v0.6.1
+// untar v0.6.3
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3032,7 +3032,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "untar",
  "namespace" : "io",
-  "version" : "v0.6.1",
+  "version" : "v0.6.3",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -3209,7 +3209,7 @@ meta = [
      "id" : "docker",
      "image" : "debian:stable-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.6.1",
+      "target_tag" : "v0.6.3",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3232,12 +3232,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/untar",
    "viash_version" : "0.9.4",
-    "git_commit" : "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea",
+    "git_commit" : "459033886f31de68cf97477867ff26e27ae6d98e",
    "git_remote" : "https://github.com/viash-hub/demultiplex"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.6.1",
+    "version" : "v0.6.3",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -3254,7 +3254,7 @@ meta = [
      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.6.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3728,7 +3728,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/demultiplex/io/untar",
-    "tag" : "v0.6.1"
+    "tag" : "v0.6.3"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/io/untar/nextflow.config
+++ b/target/nextflow/io/untar/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'io/untar'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.6.1'
+  version = 'v0.6.3'
  description = 'Unpack a .tar file. When the contents of the .tar file is just a single directory,\nput the contents of the directory into the output folder instead of that directory.\n'
 }

--- a/target/nextflow/io/untar/nextflow_labels.config
+++ b/target/nextflow/io/untar/nextflow_labels.config
@@ -21,6 +21,7 @@ process {
  withLabel: lowmem { memory = { get_memory( 8.GB * task.attempt ) } }
  withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
  withLabel: highmem { memory = { get_memory( 64.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 128.GB * task.attempt ) } }

 }

--- a/target/nextflow/runner/.config.vsh.yaml
+++ b/target/nextflow/runner/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "runner"
-version: "v0.6.1"
+version: "v0.6.3"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -217,14 +217,14 @@ build_info:
  output: "target/nextflow/runner"
  executable: "target/nextflow/runner/main.nf"
  viash_version: "0.9.4"
-  git_commit: "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea"
+  git_commit: "459033886f31de68cf97477867ff26e27ae6d98e"
  git_remote: "https://github.com/viash-hub/demultiplex"
  dependencies:
  - "target/nextflow/demultiplex"
  - "target/nextflow/io/publish"
 package_config:
  name: "demultiplex"
-  version: "v0.6.1"
+  version: "v0.6.3"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -240,7 +240,7 @@ package_config:
    )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.6.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/runner/_viash.yaml
+++ b/target/nextflow/runner/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.6.1
+version: v0.6.3
 description: |
  Demultiplexing pipeline
 license: MIT
--- a/target/nextflow/runner/main.nf
+++ b/target/nextflow/runner/main.nf
@@ -1,4 +1,4 @@
-// runner v0.6.1
+// runner v0.6.3
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3031,7 +3031,7 @@ meta = [
  "resources_dir": moduleDir.toRealPath().normalize(),
  "config": processConfig(readJsonBlob('''{
  "name" : "runner",
-  "version" : "v0.6.1",
+  "version" : "v0.6.3",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -3301,12 +3301,12 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/runner",
    "viash_version" : "0.9.4",
-    "git_commit" : "edbd04b6b129080fe2fac4d123af9ce7f1ae57ea",
+    "git_commit" : "459033886f31de68cf97477867ff26e27ae6d98e",
    "git_remote" : "https://github.com/viash-hub/demultiplex"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.6.1",
+    "version" : "v0.6.3",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -3323,7 +3323,7 @@ meta = [
      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.6.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3436,11 +3436,16 @@ workflow run_wf {
          ]
        },
        toState: { id, result, state -> [ 
-            "fastq_output": result.output, 
+            // Most of the output is copied from the input state
+            // This allows for resume functionality to work when using any of these outputs
+            // because the restult state contains a unique date in the path.
+            // Only for the sample QC ouput, multiple results are gathered 
+            // so we must use the resulting output directory.
+            "fastq_output": state.output, 
            "prefix": state.prefix,
-            "multiqc_output": result.output_multiqc,
+            "multiqc_output": state.multiqc_output,
            "sample_qc_output": result.output_sample_qc,
-            "demultiplexer_logs": result.output_demultiplexer_logs,
+            "demultiplexer_logs": state.demultiplexer_logs,
          ]
        },
        directives: [
--- a/target/nextflow/runner/nextflow.config
+++ b/target/nextflow/runner/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'runner'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.6.1'
+  version = 'v0.6.3'
  description = 'Runner for demultiplexing of raw sequencing data'
 }

--- a/target/nextflow/runner/nextflow_labels.config
+++ b/target/nextflow/runner/nextflow_labels.config
@@ -21,6 +21,7 @@ process {
  withLabel: lowmem { memory = { get_memory( 8.GB * task.attempt ) } }
  withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
  withLabel: highmem { memory = { get_memory( 64.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 128.GB * task.attempt ) } }

 }
Author	SHA1	Message	Date
CI	841f28f747	Build branch demultiplex/v0.6 with version v0.6.3 to demultiplex on branch v0.6 (4590338) Build pipeline: viash-hub.demultiplex.v0.6.3-fw6tg Source commit: `459033886f` Source message: Bump version to v0.6.3	2025-11-05 09:02:52 +00:00
CI	6646977f96	Build branch demultiplex/v0.6 with version v0.6.2 to demultiplex on branch v0.6 (16ba5d4) Build pipeline: viash-hub.demultiplex.v0.6-kgtqg Source commit: `16ba5d4283` Source message: Bump version to v0.6.2	2025-10-09 09:50:03 +00:00