Build branch v0.3 with version v0.3.11 (cd2cfac)

Build pipeline: viash-hub.demultiplex.v0.3-nwj5p Source commit: cd2cfac18e Source message: Bump version to v0.3.11
2025-05-14 09:11:58 +00:00
parent b90bd3453a
commit 194cb8d0f1
43 changed files with 501 additions and 153 deletions
--- a/target/executable/io/interop_summary_to_csv/.config.vsh.yaml
+++ b/target/executable/io/interop_summary_to_csv/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "interop_summary_to_csv"
 namespace: "io"
-version: "v0.3.10"
+version: "v0.3.11"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -41,6 +41,12 @@ resources:
 - type: "file"
  path: "nextflow_labels.config"
  dest: "nextflow_labels.config"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "iseq-DI"
 info: null
 status: "enabled"
 scope:
@@ -126,7 +132,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.10"
+  target_tag: "v0.3.11"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -151,12 +157,12 @@ build_info:
  output: "target/executable/io/interop_summary_to_csv"
  executable: "target/executable/io/interop_summary_to_csv/interop_summary_to_csv"
  viash_version: "0.9.4"
-  git_commit: "e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6"
+  git_commit: "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.10"
+  git_tag: "v0.3.10-5-gcd2cfac"
 package_config:
  name: "demultiplex"
-  version: "v0.3.10"
+  version: "v0.3.11"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -172,7 +178,7 @@ package_config:
    )'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.10'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.11'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/executable/io/interop_summary_to_csv/interop_summary_to_csv
+++ b/target/executable/io/interop_summary_to_csv/interop_summary_to_csv
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# interop_summary_to_csv v0.3.10
+# interop_summary_to_csv v0.3.11
 # 
 # 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="2025-05-07T11:20:11Z"
+LABEL org.opencontainers.image.created="2025-05-14T08:46:02Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6"
-LABEL org.opencontainers.image.version="v0.3.10"
+LABEL org.opencontainers.image.revision="cd2cfac18e14622e1a5d7a0d489f64c30e83dab2"
+LABEL org.opencontainers.image.version="v0.3.11"

 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 v0.3.10"
+  echo "interop_summary_to_csv v0.3.11"
  echo ""
  echo "Input arguments:"
  echo "    --input"
@@ -635,7 +635,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "interop_summary_to_csv v0.3.10"
+            echo "interop_summary_to_csv v0.3.11"
            exit
            ;;
        --input)
@@ -759,7 +759,7 @@ if [[ "$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:v0.3.10'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/interop_summary_to_csv:v0.3.11'
  fi

  # print dockerfile
--- a/target/executable/io/publish/.config.vsh.yaml
+++ b/target/executable/io/publish/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "publish"
 namespace: "io"
-version: "v0.3.10"
+version: "v0.3.11"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -44,6 +44,15 @@ argument_groups:
    direction: "input"
    multiple: false
    multiple_sep: ";"
+  - type: "file"
+    name: "--input_demultiplexer_logs"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
 - name: "Output arguments"
  arguments:
  - type: "file"
@@ -90,6 +99,17 @@ argument_groups:
    direction: "output"
    multiple: false
    multiple_sep: ";"
+  - type: "file"
+    name: "--output_demultiplexer_logs"
+    info: null
+    default:
+    - "demultiplexer_logs"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
 resources:
 - type: "bash_script"
  path: "code.sh"
@@ -181,7 +201,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.10"
+  target_tag: "v0.3.11"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -199,12 +219,12 @@ build_info:
  output: "target/executable/io/publish"
  executable: "target/executable/io/publish/publish"
  viash_version: "0.9.4"
-  git_commit: "e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6"
+  git_commit: "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.10"
+  git_tag: "v0.3.10-5-gcd2cfac"
 package_config:
  name: "demultiplex"
-  version: "v0.3.10"
+  version: "v0.3.11"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -220,7 +240,7 @@ package_config:
    )'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.10'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.11'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/executable/io/publish/publish
+++ b/target/executable/io/publish/publish
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# publish v0.3.10
+# publish v0.3.11
 # 
 # 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="2025-05-07T11:20:10Z"
+LABEL org.opencontainers.image.created="2025-05-14T08:46:03Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6"
-LABEL org.opencontainers.image.version="v0.3.10"
+LABEL org.opencontainers.image.revision="cd2cfac18e14622e1a5d7a0d489f64c30e83dab2"
+LABEL org.opencontainers.image.version="v0.3.11"

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

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "publish v0.3.10"
+  echo "publish v0.3.11"
  echo ""
  echo "Publish the processed results of the run"
  echo ""
@@ -591,6 +591,9 @@ function ViashHelp {
  echo "        type: file, required parameter, file must exist"
  echo "        Location where to write the run information to."
  echo ""
+  echo "    --input_demultiplexer_logs"
+  echo "        type: file, required parameter, file must exist"
+  echo ""
  echo "Output arguments:"
  echo "    --output"
  echo "        type: file, output, file must exist"
@@ -608,6 +611,10 @@ function ViashHelp {
  echo "        type: file, output, file must exist"
  echo "        default: run_information.csv"
  echo ""
+  echo "    --output_demultiplexer_logs"
+  echo "        type: file, output, file must exist"
+  echo "        default: demultiplexer_logs"
+  echo ""
  echo "Viash built in Computational Requirements:"
  echo "    ---cpus=INT"
  echo "        Number of CPUs to use"
@@ -655,7 +662,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "publish v0.3.10"
+            echo "publish v0.3.11"
            exit
            ;;
        --input)
@@ -708,6 +715,17 @@ while [[ $# -gt 0 ]]; do
            VIASH_PAR_INPUT_RUN_INFORMATION=$(ViashRemoveFlags "$1")
            shift 1
            ;;
+        --input_demultiplexer_logs)
+            [ -n "$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS" ] && ViashError Bad arguments for option \'--input_demultiplexer_logs\': \'$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --input_demultiplexer_logs. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --input_demultiplexer_logs=*)
+            [ -n "$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS" ] && ViashError Bad arguments for option \'--input_demultiplexer_logs=*\': \'$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
        --output)
            [ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--output\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT="$2"
@@ -752,6 +770,17 @@ while [[ $# -gt 0 ]]; do
            VIASH_PAR_OUTPUT_RUN_INFORMATION=$(ViashRemoveFlags "$1")
            shift 1
            ;;
+        --output_demultiplexer_logs)
+            [ -n "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS" ] && ViashError Bad arguments for option \'--output_demultiplexer_logs\': \'$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --output_demultiplexer_logs. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --output_demultiplexer_logs=*)
+            [ -n "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS" ] && ViashError Bad arguments for option \'--output_demultiplexer_logs=*\': \'$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
        ---engine)
            VIASH_ENGINE_ID="$2"
            shift 2
@@ -840,7 +869,7 @@ if [[ "$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:v0.3.10'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/publish:v0.3.11'
  fi

  # print dockerfile
@@ -940,6 +969,10 @@ if [ -z ${VIASH_PAR_INPUT_RUN_INFORMATION+x} ]; then
  ViashError '--input_run_information' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
 fi
+if [ -z ${VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS+x} ]; then
+  ViashError '--input_demultiplexer_logs' is a required argument. Use "--help" to get more information on the parameters.
+  exit 1
+fi
 if [ -z ${VIASH_META_NAME+x} ]; then
  ViashError 'name' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
@@ -978,6 +1011,9 @@ fi
 if [ -z ${VIASH_PAR_OUTPUT_RUN_INFORMATION+x} ]; then
  VIASH_PAR_OUTPUT_RUN_INFORMATION="run_information.csv"
 fi
+if [ -z ${VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS+x} ]; then
+  VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS="demultiplexer_logs"
+fi

 # check whether required files exist
 if [ ! -z "$VIASH_PAR_INPUT" ] && [ ! -e "$VIASH_PAR_INPUT" ]; then
@@ -1004,6 +1040,10 @@ if [ ! -z "$VIASH_PAR_INPUT_RUN_INFORMATION" ] && [ ! -e "$VIASH_PAR_INPUT_RUN_I
  ViashError "Input file '$VIASH_PAR_INPUT_RUN_INFORMATION' does not exist."
  exit 1
 fi
+if [ ! -z "$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS" ] && [ ! -e "$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS" ]; then
+  ViashError "Input file '$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS' does not exist."
+  exit 1
+fi

 # check whether parameters values are of the right type
 if [[ -n "$VIASH_META_CPUS" ]]; then
@@ -1092,6 +1132,9 @@ fi
 if [ ! -z "$VIASH_PAR_OUTPUT_RUN_INFORMATION" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT_RUN_INFORMATION")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_OUTPUT_RUN_INFORMATION")"
 fi
+if [ ! -z "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS")" ]; then
+  mkdir -p "$(dirname "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS")"
+fi

 if  [ "$VIASH_ENGINE_ID" == "native" ]  ; then
  if [ "$VIASH_MODE" == "run" ]; then
@@ -1128,6 +1171,10 @@ if [ ! -z "$VIASH_PAR_INPUT_RUN_INFORMATION" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INPUT_RUN_INFORMATION")" )
  VIASH_PAR_INPUT_RUN_INFORMATION=$(ViashDockerAutodetectMount "$VIASH_PAR_INPUT_RUN_INFORMATION")
 fi
+if [ ! -z "$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS")" )
+  VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS=$(ViashDockerAutodetectMount "$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS")
+fi
 if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT")" )
  VIASH_PAR_OUTPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT")
@@ -1148,6 +1195,11 @@ if [ ! -z "$VIASH_PAR_OUTPUT_RUN_INFORMATION" ]; then
  VIASH_PAR_OUTPUT_RUN_INFORMATION=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT_RUN_INFORMATION")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT_RUN_INFORMATION" )
 fi
+if [ ! -z "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS")" )
+  VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS")
+  VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS" )
+fi
 if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_RESOURCES_DIR")" )
  VIASH_META_RESOURCES_DIR=$(ViashDockerAutodetectMount "$VIASH_META_RESOURCES_DIR")
@@ -1221,10 +1273,12 @@ $( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "${VIASH_PAR_INPUT}" | sed "s#'#'
 $( if [ ! -z ${VIASH_PAR_INPUT_FALCO+x} ]; then echo "${VIASH_PAR_INPUT_FALCO}" | sed "s#'#'\"'\"'#g;s#.*#par_input_falco='&'#" ; else echo "# par_input_falco="; fi )
 $( if [ ! -z ${VIASH_PAR_INPUT_MULTIQC+x} ]; then echo "${VIASH_PAR_INPUT_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_input_multiqc='&'#" ; else echo "# par_input_multiqc="; fi )
 $( if [ ! -z ${VIASH_PAR_INPUT_RUN_INFORMATION+x} ]; then echo "${VIASH_PAR_INPUT_RUN_INFORMATION}" | sed "s#'#'\"'\"'#g;s#.*#par_input_run_information='&'#" ; else echo "# par_input_run_information="; fi )
+$( if [ ! -z ${VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS+x} ]; then echo "${VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS}" | sed "s#'#'\"'\"'#g;s#.*#par_input_demultiplexer_logs='&'#" ; else echo "# par_input_demultiplexer_logs="; fi )
 $( if [ ! -z ${VIASH_PAR_OUTPUT+x} ]; then echo "${VIASH_PAR_OUTPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_output='&'#" ; else echo "# par_output="; fi )
 $( if [ ! -z ${VIASH_PAR_OUTPUT_FALCO+x} ]; then echo "${VIASH_PAR_OUTPUT_FALCO}" | sed "s#'#'\"'\"'#g;s#.*#par_output_falco='&'#" ; else echo "# par_output_falco="; fi )
 $( if [ ! -z ${VIASH_PAR_OUTPUT_MULTIQC+x} ]; then echo "${VIASH_PAR_OUTPUT_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_output_multiqc='&'#" ; else echo "# par_output_multiqc="; fi )
 $( if [ ! -z ${VIASH_PAR_OUTPUT_RUN_INFORMATION+x} ]; then echo "${VIASH_PAR_OUTPUT_RUN_INFORMATION}" | sed "s#'#'\"'\"'#g;s#.*#par_output_run_information='&'#" ; else echo "# par_output_run_information="; fi )
+$( if [ ! -z ${VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS+x} ]; then echo "${VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS}" | sed "s#'#'\"'\"'#g;s#.*#par_output_demultiplexer_logs='&'#" ; else echo "# par_output_demultiplexer_logs="; fi )
 $( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi )
 $( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi )
 $( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "${VIASH_META_RESOURCES_DIR}" | sed "s#'#'\"'\"'#g;s#.*#meta_resources_dir='&'#" ; else echo "# meta_resources_dir="; fi )
@@ -1252,6 +1306,7 @@ set -eo pipefail
 declare -A input_output_mapping=(["par_input"]="par_output" 
                                 ["par_input_multiqc"]="par_output_multiqc"
                                 ["par_input_run_information"]="par_output_run_information"
+                                 ["par_input_demultiplexer_logs"]="par_output_demultiplexer_logs"
                                )

 for input_argument_name in "\${!input_output_mapping[@]}"
@@ -1310,6 +1365,9 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  if [ ! -z "$VIASH_PAR_INPUT_RUN_INFORMATION" ]; then
    VIASH_PAR_INPUT_RUN_INFORMATION=$(ViashDockerStripAutomount "$VIASH_PAR_INPUT_RUN_INFORMATION")
  fi
+  if [ ! -z "$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS" ]; then
+    VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS=$(ViashDockerStripAutomount "$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS")
+  fi
  if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
    VIASH_PAR_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT")
  fi
@@ -1322,6 +1380,9 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  if [ ! -z "$VIASH_PAR_OUTPUT_RUN_INFORMATION" ]; then
    VIASH_PAR_OUTPUT_RUN_INFORMATION=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT_RUN_INFORMATION")
  fi
+  if [ ! -z "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS" ]; then
+    VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS")
+  fi
  if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
    VIASH_META_RESOURCES_DIR=$(ViashDockerStripAutomount "$VIASH_META_RESOURCES_DIR")
  fi
@@ -1354,6 +1415,10 @@ if [ ! -z "$VIASH_PAR_OUTPUT_RUN_INFORMATION" ] && [ ! -e "$VIASH_PAR_OUTPUT_RUN
  ViashError "Output file '$VIASH_PAR_OUTPUT_RUN_INFORMATION' does not exist."
  exit 1
 fi
+if [ ! -z "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS" ] && [ ! -e "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS" ]; then
+  ViashError "Output file '$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS' does not exist."
+  exit 1
+fi


 exit 0
--- a/target/executable/io/untar/.config.vsh.yaml
+++ b/target/executable/io/untar/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "untar"
 namespace: "io"
-version: "v0.3.10"
+version: "v0.3.11"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -138,7 +138,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.10"
+  target_tag: "v0.3.11"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -156,12 +156,12 @@ build_info:
  output: "target/executable/io/untar"
  executable: "target/executable/io/untar/untar"
  viash_version: "0.9.4"
-  git_commit: "e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6"
+  git_commit: "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.3.10"
+  git_tag: "v0.3.10-5-gcd2cfac"
 package_config:
  name: "demultiplex"
-  version: "v0.3.10"
+  version: "v0.3.11"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
@@ -177,7 +177,7 @@ package_config:
    )'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.3.10'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.11'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/executable/io/untar/untar
+++ b/target/executable/io/untar/untar
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# untar v0.3.10
+# untar v0.3.11
 # 
 # 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="2025-05-07T11:20:10Z"
+LABEL org.opencontainers.image.created="2025-05-14T08:46:02Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6"
-LABEL org.opencontainers.image.version="v0.3.10"
+LABEL org.opencontainers.image.revision="cd2cfac18e14622e1a5d7a0d489f64c30e83dab2"
+LABEL org.opencontainers.image.version="v0.3.11"

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

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "untar v0.3.10"
+  echo "untar v0.3.11"
  echo ""
  echo "Unpack a .tar file. When the contents of the .tar file is just a single"
  echo "directory,"
@@ -641,7 +641,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "untar v0.3.10"
+            echo "untar v0.3.11"
            exit
            ;;
        --input)
@@ -771,7 +771,7 @@ if [[ "$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:v0.3.10'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/untar:v0.3.11'
  fi

  # print dockerfile