Build branch main with version main (5705b88)

Build pipeline: viash-hub.craftbox.main-6n7js Source commit: 5705b88fa2 Source message: Bump Viash and update CHANGELOG
2024-09-12 15:47:36 +00:00
parent 5e403dd5d9
commit 108879b9f9
14 changed files with 311 additions and 159 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,8 @@

 ## NEW FEATURES

+* `concat_text`: Concatenate a number of text files
+
 * `csv2fasta`: Convert two columns from a CSV file to FASTA entries (PR #1).

 * `untar`: Unpack a .tar file. When the contents of the .tar file is just a single directory,
@@ -9,4 +11,4 @@

 ## MINOR CHANGES

-* Bump viash to 0.9.0-RC7 (PR #6).
+* Bump viash to 0.9.0
--- a/target/executable/concat_text/.config.vsh.yaml
+++ b/target/executable/concat_text/.config.vsh.yaml
@@ -170,15 +170,15 @@ build_info:
  engine: "docker|native"
  output: "target/executable/concat_text"
  executable: "target/executable/concat_text/concat_text"
-  viash_version: "0.9.0-RC6"
-  git_commit: "373be82129c13f50558c0dae25c07afe0866a8ba"
+  viash_version: "0.9.0-RC7"
+  git_commit: "5705b88fa20f267475b5d0ae1ca25dbf55ff1295"
  git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
  name: "craftbox"
  version: "main"
  description: "A collection of custom-tailored scripts and applied tools.\n"
  info: null
-  viash_version: "0.9.0-RC6"
+  viash_version: "0.9.0-RC7"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/concat_text/concat_text
+++ b/target/executable/concat_text/concat_text
@@ -2,7 +2,7 @@

 # concat_text main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC6 and is thus a
+# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
 # derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
 # Data Intuitive.
 # 
@@ -58,24 +58,24 @@ function ViashRemoveFlags {
 # $1      : Should always be set to ${BASH_SOURCE[0]}
 # returns : The absolute path of the bash file
 function ViashSourceDir {
-  SOURCE="$1"
-  while [ -h "$SOURCE" ]; do
-    DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )"
-    SOURCE="$(readlink "$SOURCE")"
-    [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE"
+  local source="$1"
+  while [ -h "$source" ]; do
+    local dir="$( cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd )"
+    source="$(readlink "$source")"
+    [[ $source != /* ]] && source="$dir/$source"
  done
-  cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd
+  cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd
 }
 # ViashFindTargetDir: return the path of the '.build.yaml' file, following symlinks
 # usage   : ViashFindTargetDir 'ScriptPath'
 # $1      : The location from where to start the upward search
 # returns : The absolute path of the '.build.yaml' file
 function ViashFindTargetDir {
-  SOURCE="$1"
-  while [[ "$SOURCE" != "" && ! -e "$SOURCE/.build.yaml" ]]; do
-    SOURCE=${SOURCE%/*}
+  local source="$1"
+  while [[ "$source" != "" && ! -e "$source/.build.yaml" ]]; do
+    source=${source%/*}
  done
-  echo $SOURCE
+  echo $source
 }
 # see https://en.wikipedia.org/wiki/Syslog#Severity_level
 VIASH_LOGCODE_EMERGENCY=0
@@ -219,9 +219,9 @@ function ViashDockerInstallationCheck {
  fi

  ViashDebug "Checking whether the Docker daemon is running"
-  save=$-; set +e
-  docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
-  out=$?
+  local save=$-; set +e
+  local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
+  local out=$?
  [[ $save =~ e ]] && set -e
  if [ $out -ne 0 ]; then
    ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
@@ -273,9 +273,9 @@ function ViashDockerPull {
  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
    docker pull $1 && return 0 || return 1
  else
-    save=$-; set +e
+    local save=$-; set +e
    docker pull $1 2> /dev/null > /dev/null
-    out=$?
+    local out=$?
    [[ $save =~ e ]] && set -e
    if [ $out -ne 0 ]; then
      ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
@@ -295,7 +295,8 @@ function ViashDockerPull {
 #   echo $?                                     # returns '1'
 function ViashDockerPush {
  ViashNotice "Pushing image to '$1'"
-  save=$-; set +e
+  local save=$-; set +e
+  local out
  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
    docker push $1
    out=$?
@@ -319,9 +320,9 @@ function ViashDockerPush {
 # examples:
 #   ViashDockerPullElseBuild mynewcomponent
 function ViashDockerPullElseBuild {
-  save=$-; set +e
+  local save=$-; set +e
  ViashDockerPull $1
-  out=$?
+  local out=$?
  [[ $save =~ e ]] && set -e
  if [ $out -ne 0 ]; then
    ViashDockerBuild $@
@@ -478,9 +479,9 @@ RUN apk add --no-cache bash procps file

 LABEL org.opencontainers.image.authors="Toni Verbeiren, Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component concat_text"
-LABEL org.opencontainers.image.created="2024-08-19T07:26:27Z"
+LABEL org.opencontainers.image.created="2024-09-12T15:41:16Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/craftbox"
-LABEL org.opencontainers.image.revision="373be82129c13f50558c0dae25c07afe0866a8ba"
+LABEL org.opencontainers.image.revision="5705b88fa20f267475b5d0ae1ca25dbf55ff1295"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
@@ -507,6 +508,9 @@ function ViashDockerBuildArgs {
 #   ViashAbsolutePath /foo/bar/..     # returns /foo
 function ViashAbsolutePath {
  local thePath
+  local parr
+  local outp
+  local len
  if [[ ! "$1" =~ ^/ ]]; then
    thePath="$PWD/$1"
  else
@@ -537,14 +541,17 @@ function ViashAbsolutePath {
  )
 }
 # ViashDockerAutodetectMount: auto configuring docker mounts from parameters
-# $1                  : The parameter value
-# returns             : New parameter
-# $VIASH_DIRECTORY_MOUNTS : Added another parameter to be passed to docker
+# $1                             : The parameter value
+# returns                        : New parameter
+# $VIASH_DIRECTORY_MOUNTS        : Added another parameter to be passed to docker
+# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
 # examples:
 #   ViashDockerAutodetectMount /path/to/bar      # returns '/viash_automount/path/to/bar'
 #   ViashDockerAutodetectMountArg /path/to/bar   # returns '--volume="/path/to:/viash_automount/path/to"'
 function ViashDockerAutodetectMount {
-  abs_path=$(ViashAbsolutePath "$1")
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
  if [ -d "$abs_path" ]; then
    mount_source="$abs_path"
    base_name=""
@@ -552,7 +559,7 @@ function ViashDockerAutodetectMount {
    mount_source=`dirname "$abs_path"`
    base_name=`basename "$abs_path"`
  fi
-  mount_target="/viash_automount$mount_source"
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
  if [ -z "$base_name" ]; then
    echo "$mount_target"
  else
@@ -560,7 +567,9 @@ function ViashDockerAutodetectMount {
  fi
 }
 function ViashDockerAutodetectMountArg {
-  abs_path=$(ViashAbsolutePath "$1")
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
  if [ -d "$abs_path" ]; then
    mount_source="$abs_path"
    base_name=""
@@ -568,17 +577,22 @@ function ViashDockerAutodetectMountArg {
    mount_source=`dirname "$abs_path"`
    base_name=`basename "$abs_path"`
  fi
-  mount_target="/viash_automount$mount_source"
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
  ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
  echo "--volume=\"$mount_source:$mount_target\""
 }
 function ViashDockerStripAutomount {
-  abs_path=$(ViashAbsolutePath "$1")
-  echo "${abs_path#/viash_automount}"
+  local abs_path=$(ViashAbsolutePath "$1")
+  echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}"
 }
 # initialise variables
 VIASH_DIRECTORY_MOUNTS=()

+# configure default docker automount prefix if it is unset
+if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then
+  VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount"
+fi
+
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)

@@ -662,6 +676,18 @@ while [[ $# -gt 0 ]]; do
            VIASH_MODE='dockerfile'
            shift 1
            ;;
+        ---docker_run_args)
+            VIASH_DOCKER_RUN_ARGS+=("$2")
+            shift 2
+            ;;
+        ---docker_run_args=*)
+            VIASH_DOCKER_RUN_ARGS+=("$(ViashRemoveFlags "$1")")
+            shift 1
+            ;;
+        ---docker_image_id)
+            VIASH_MODE='docker_image_id'
+            shift 1
+            ;;
        ---debug)
            VIASH_MODE='debug'
            shift 1
@@ -723,6 +749,10 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  if [ "$VIASH_MODE" == "dockerfile" ]; then
    ViashDockerfile "$VIASH_ENGINE_ID"
    exit 0
+
+  elif [ "$VIASH_MODE" == "docker_image_id" ]; then
+    echo "$VIASH_DOCKER_IMAGE_ID"
+    exit 0
  
  # enter docker container
  elif [[ "$VIASH_MODE" == "debug" ]]; then
--- a/target/executable/csv2fasta/.config.vsh.yaml
+++ b/target/executable/csv2fasta/.config.vsh.yaml
@@ -221,15 +221,15 @@ build_info:
  engine: "docker|native"
  output: "target/executable/csv2fasta"
  executable: "target/executable/csv2fasta/csv2fasta"
-  viash_version: "0.9.0-RC6"
-  git_commit: "373be82129c13f50558c0dae25c07afe0866a8ba"
+  viash_version: "0.9.0-RC7"
+  git_commit: "5705b88fa20f267475b5d0ae1ca25dbf55ff1295"
  git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
  name: "craftbox"
  version: "main"
  description: "A collection of custom-tailored scripts and applied tools.\n"
  info: null
-  viash_version: "0.9.0-RC6"
+  viash_version: "0.9.0-RC7"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/csv2fasta/csv2fasta
+++ b/target/executable/csv2fasta/csv2fasta
@@ -2,7 +2,7 @@

 # csv2fasta main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC6 and is thus a
+# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
 # derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
 # Data Intuitive.
 # 
@@ -54,24 +54,24 @@ function ViashRemoveFlags {
 # $1      : Should always be set to ${BASH_SOURCE[0]}
 # returns : The absolute path of the bash file
 function ViashSourceDir {
-  SOURCE="$1"
-  while [ -h "$SOURCE" ]; do
-    DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )"
-    SOURCE="$(readlink "$SOURCE")"
-    [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE"
+  local source="$1"
+  while [ -h "$source" ]; do
+    local dir="$( cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd )"
+    source="$(readlink "$source")"
+    [[ $source != /* ]] && source="$dir/$source"
  done
-  cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd
+  cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd
 }
 # ViashFindTargetDir: return the path of the '.build.yaml' file, following symlinks
 # usage   : ViashFindTargetDir 'ScriptPath'
 # $1      : The location from where to start the upward search
 # returns : The absolute path of the '.build.yaml' file
 function ViashFindTargetDir {
-  SOURCE="$1"
-  while [[ "$SOURCE" != "" && ! -e "$SOURCE/.build.yaml" ]]; do
-    SOURCE=${SOURCE%/*}
+  local source="$1"
+  while [[ "$source" != "" && ! -e "$source/.build.yaml" ]]; do
+    source=${source%/*}
  done
-  echo $SOURCE
+  echo $source
 }
 # see https://en.wikipedia.org/wiki/Syslog#Severity_level
 VIASH_LOGCODE_EMERGENCY=0
@@ -261,9 +261,9 @@ function ViashDockerInstallationCheck {
  fi

  ViashDebug "Checking whether the Docker daemon is running"
-  save=$-; set +e
-  docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
-  out=$?
+  local save=$-; set +e
+  local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
+  local out=$?
  [[ $save =~ e ]] && set -e
  if [ $out -ne 0 ]; then
    ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
@@ -315,9 +315,9 @@ function ViashDockerPull {
  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
    docker pull $1 && return 0 || return 1
  else
-    save=$-; set +e
+    local save=$-; set +e
    docker pull $1 2> /dev/null > /dev/null
-    out=$?
+    local out=$?
    [[ $save =~ e ]] && set -e
    if [ $out -ne 0 ]; then
      ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
@@ -337,7 +337,8 @@ function ViashDockerPull {
 #   echo $?                                     # returns '1'
 function ViashDockerPush {
  ViashNotice "Pushing image to '$1'"
-  save=$-; set +e
+  local save=$-; set +e
+  local out
  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
    docker push $1
    out=$?
@@ -361,9 +362,9 @@ function ViashDockerPush {
 # examples:
 #   ViashDockerPullElseBuild mynewcomponent
 function ViashDockerPullElseBuild {
-  save=$-; set +e
+  local save=$-; set +e
  ViashDockerPull $1
-  out=$?
+  local out=$?
  [[ $save =~ e ]] && set -e
  if [ $out -ne 0 ]; then
    ViashDockerBuild $@
@@ -524,9 +525,9 @@ RUN pip install --upgrade pip && \
  pip install --upgrade --no-cache-dir "dnaio"

 LABEL org.opencontainers.image.description="Companion container for running component csv2fasta"
-LABEL org.opencontainers.image.created="2024-08-19T07:26:26Z"
+LABEL org.opencontainers.image.created="2024-09-12T15:41:15Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/craftbox"
-LABEL org.opencontainers.image.revision="373be82129c13f50558c0dae25c07afe0866a8ba"
+LABEL org.opencontainers.image.revision="5705b88fa20f267475b5d0ae1ca25dbf55ff1295"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
@@ -553,6 +554,9 @@ function ViashDockerBuildArgs {
 #   ViashAbsolutePath /foo/bar/..     # returns /foo
 function ViashAbsolutePath {
  local thePath
+  local parr
+  local outp
+  local len
  if [[ ! "$1" =~ ^/ ]]; then
    thePath="$PWD/$1"
  else
@@ -583,14 +587,17 @@ function ViashAbsolutePath {
  )
 }
 # ViashDockerAutodetectMount: auto configuring docker mounts from parameters
-# $1                  : The parameter value
-# returns             : New parameter
-# $VIASH_DIRECTORY_MOUNTS : Added another parameter to be passed to docker
+# $1                             : The parameter value
+# returns                        : New parameter
+# $VIASH_DIRECTORY_MOUNTS        : Added another parameter to be passed to docker
+# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
 # examples:
 #   ViashDockerAutodetectMount /path/to/bar      # returns '/viash_automount/path/to/bar'
 #   ViashDockerAutodetectMountArg /path/to/bar   # returns '--volume="/path/to:/viash_automount/path/to"'
 function ViashDockerAutodetectMount {
-  abs_path=$(ViashAbsolutePath "$1")
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
  if [ -d "$abs_path" ]; then
    mount_source="$abs_path"
    base_name=""
@@ -598,7 +605,7 @@ function ViashDockerAutodetectMount {
    mount_source=`dirname "$abs_path"`
    base_name=`basename "$abs_path"`
  fi
-  mount_target="/viash_automount$mount_source"
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
  if [ -z "$base_name" ]; then
    echo "$mount_target"
  else
@@ -606,7 +613,9 @@ function ViashDockerAutodetectMount {
  fi
 }
 function ViashDockerAutodetectMountArg {
-  abs_path=$(ViashAbsolutePath "$1")
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
  if [ -d "$abs_path" ]; then
    mount_source="$abs_path"
    base_name=""
@@ -614,17 +623,22 @@ function ViashDockerAutodetectMountArg {
    mount_source=`dirname "$abs_path"`
    base_name=`basename "$abs_path"`
  fi
-  mount_target="/viash_automount$mount_source"
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
  ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
  echo "--volume=\"$mount_source:$mount_target\""
 }
 function ViashDockerStripAutomount {
-  abs_path=$(ViashAbsolutePath "$1")
-  echo "${abs_path#/viash_automount}"
+  local abs_path=$(ViashAbsolutePath "$1")
+  echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}"
 }
 # initialise variables
 VIASH_DIRECTORY_MOUNTS=()

+# configure default docker automount prefix if it is unset
+if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then
+  VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount"
+fi
+
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)

@@ -768,6 +782,18 @@ while [[ $# -gt 0 ]]; do
            VIASH_MODE='dockerfile'
            shift 1
            ;;
+        ---docker_run_args)
+            VIASH_DOCKER_RUN_ARGS+=("$2")
+            shift 2
+            ;;
+        ---docker_run_args=*)
+            VIASH_DOCKER_RUN_ARGS+=("$(ViashRemoveFlags "$1")")
+            shift 1
+            ;;
+        ---docker_image_id)
+            VIASH_MODE='docker_image_id'
+            shift 1
+            ;;
        ---debug)
            VIASH_MODE='debug'
            shift 1
@@ -829,6 +855,10 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  if [ "$VIASH_MODE" == "dockerfile" ]; then
    ViashDockerfile "$VIASH_ENGINE_ID"
    exit 0
+
+  elif [ "$VIASH_MODE" == "docker_image_id" ]; then
+    echo "$VIASH_DOCKER_IMAGE_ID"
+    exit 0
  
  # enter docker container
  elif [[ "$VIASH_MODE" == "debug" ]]; then
--- a/target/executable/untar/.config.vsh.yaml
+++ b/target/executable/untar/.config.vsh.yaml
@@ -146,15 +146,15 @@ build_info:
  engine: "docker|native"
  output: "target/executable/untar"
  executable: "target/executable/untar/untar"
-  viash_version: "0.9.0-RC6"
-  git_commit: "373be82129c13f50558c0dae25c07afe0866a8ba"
+  viash_version: "0.9.0-RC7"
+  git_commit: "5705b88fa20f267475b5d0ae1ca25dbf55ff1295"
  git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
  name: "craftbox"
  version: "main"
  description: "A collection of custom-tailored scripts and applied tools.\n"
  info: null
-  viash_version: "0.9.0-RC6"
+  viash_version: "0.9.0-RC7"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/untar/untar
+++ b/target/executable/untar/untar
@@ -2,7 +2,7 @@

 # untar main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC6 and is thus a
+# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
 # derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
 # Data Intuitive.
 # 
@@ -54,24 +54,24 @@ function ViashRemoveFlags {
 # $1      : Should always be set to ${BASH_SOURCE[0]}
 # returns : The absolute path of the bash file
 function ViashSourceDir {
-  SOURCE="$1"
-  while [ -h "$SOURCE" ]; do
-    DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )"
-    SOURCE="$(readlink "$SOURCE")"
-    [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE"
+  local source="$1"
+  while [ -h "$source" ]; do
+    local dir="$( cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd )"
+    source="$(readlink "$source")"
+    [[ $source != /* ]] && source="$dir/$source"
  done
-  cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd
+  cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd
 }
 # ViashFindTargetDir: return the path of the '.build.yaml' file, following symlinks
 # usage   : ViashFindTargetDir 'ScriptPath'
 # $1      : The location from where to start the upward search
 # returns : The absolute path of the '.build.yaml' file
 function ViashFindTargetDir {
-  SOURCE="$1"
-  while [[ "$SOURCE" != "" && ! -e "$SOURCE/.build.yaml" ]]; do
-    SOURCE=${SOURCE%/*}
+  local source="$1"
+  while [[ "$source" != "" && ! -e "$source/.build.yaml" ]]; do
+    source=${source%/*}
  done
-  echo $SOURCE
+  echo $source
 }
 # see https://en.wikipedia.org/wiki/Syslog#Severity_level
 VIASH_LOGCODE_EMERGENCY=0
@@ -215,9 +215,9 @@ function ViashDockerInstallationCheck {
  fi

  ViashDebug "Checking whether the Docker daemon is running"
-  save=$-; set +e
-  docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
-  out=$?
+  local save=$-; set +e
+  local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
+  local out=$?
  [[ $save =~ e ]] && set -e
  if [ $out -ne 0 ]; then
    ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
@@ -269,9 +269,9 @@ function ViashDockerPull {
  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
    docker pull $1 && return 0 || return 1
  else
-    save=$-; set +e
+    local save=$-; set +e
    docker pull $1 2> /dev/null > /dev/null
-    out=$?
+    local out=$?
    [[ $save =~ e ]] && set -e
    if [ $out -ne 0 ]; then
      ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
@@ -291,7 +291,8 @@ function ViashDockerPull {
 #   echo $?                                     # returns '1'
 function ViashDockerPush {
  ViashNotice "Pushing image to '$1'"
-  save=$-; set +e
+  local save=$-; set +e
+  local out
  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
    docker push $1
    out=$?
@@ -315,9 +316,9 @@ function ViashDockerPush {
 # examples:
 #   ViashDockerPullElseBuild mynewcomponent
 function ViashDockerPullElseBuild {
-  save=$-; set +e
+  local save=$-; set +e
  ViashDockerPull $1
-  out=$?
+  local out=$?
  [[ $save =~ e ]] && set -e
  if [ $out -ne 0 ]; then
    ViashDockerBuild $@
@@ -475,9 +476,9 @@ RUN apt-get update && \
  rm -rf /var/lib/apt/lists/*

 LABEL org.opencontainers.image.description="Companion container for running component untar"
-LABEL org.opencontainers.image.created="2024-08-19T07:26:27Z"
+LABEL org.opencontainers.image.created="2024-09-12T15:41:15Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/craftbox"
-LABEL org.opencontainers.image.revision="373be82129c13f50558c0dae25c07afe0866a8ba"
+LABEL org.opencontainers.image.revision="5705b88fa20f267475b5d0ae1ca25dbf55ff1295"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
@@ -504,6 +505,9 @@ function ViashDockerBuildArgs {
 #   ViashAbsolutePath /foo/bar/..     # returns /foo
 function ViashAbsolutePath {
  local thePath
+  local parr
+  local outp
+  local len
  if [[ ! "$1" =~ ^/ ]]; then
    thePath="$PWD/$1"
  else
@@ -534,14 +538,17 @@ function ViashAbsolutePath {
  )
 }
 # ViashDockerAutodetectMount: auto configuring docker mounts from parameters
-# $1                  : The parameter value
-# returns             : New parameter
-# $VIASH_DIRECTORY_MOUNTS : Added another parameter to be passed to docker
+# $1                             : The parameter value
+# returns                        : New parameter
+# $VIASH_DIRECTORY_MOUNTS        : Added another parameter to be passed to docker
+# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
 # examples:
 #   ViashDockerAutodetectMount /path/to/bar      # returns '/viash_automount/path/to/bar'
 #   ViashDockerAutodetectMountArg /path/to/bar   # returns '--volume="/path/to:/viash_automount/path/to"'
 function ViashDockerAutodetectMount {
-  abs_path=$(ViashAbsolutePath "$1")
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
  if [ -d "$abs_path" ]; then
    mount_source="$abs_path"
    base_name=""
@@ -549,7 +556,7 @@ function ViashDockerAutodetectMount {
    mount_source=`dirname "$abs_path"`
    base_name=`basename "$abs_path"`
  fi
-  mount_target="/viash_automount$mount_source"
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
  if [ -z "$base_name" ]; then
    echo "$mount_target"
  else
@@ -557,7 +564,9 @@ function ViashDockerAutodetectMount {
  fi
 }
 function ViashDockerAutodetectMountArg {
-  abs_path=$(ViashAbsolutePath "$1")
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
  if [ -d "$abs_path" ]; then
    mount_source="$abs_path"
    base_name=""
@@ -565,17 +574,22 @@ function ViashDockerAutodetectMountArg {
    mount_source=`dirname "$abs_path"`
    base_name=`basename "$abs_path"`
  fi
-  mount_target="/viash_automount$mount_source"
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
  ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
  echo "--volume=\"$mount_source:$mount_target\""
 }
 function ViashDockerStripAutomount {
-  abs_path=$(ViashAbsolutePath "$1")
-  echo "${abs_path#/viash_automount}"
+  local abs_path=$(ViashAbsolutePath "$1")
+  echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}"
 }
 # initialise variables
 VIASH_DIRECTORY_MOUNTS=()

+# configure default docker automount prefix if it is unset
+if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then
+  VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount"
+fi
+
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)

@@ -665,6 +679,18 @@ while [[ $# -gt 0 ]]; do
            VIASH_MODE='dockerfile'
            shift 1
            ;;
+        ---docker_run_args)
+            VIASH_DOCKER_RUN_ARGS+=("$2")
+            shift 2
+            ;;
+        ---docker_run_args=*)
+            VIASH_DOCKER_RUN_ARGS+=("$(ViashRemoveFlags "$1")")
+            shift 1
+            ;;
+        ---docker_image_id)
+            VIASH_MODE='docker_image_id'
+            shift 1
+            ;;
        ---debug)
            VIASH_MODE='debug'
            shift 1
@@ -726,6 +752,10 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  if [ "$VIASH_MODE" == "dockerfile" ]; then
    ViashDockerfile "$VIASH_ENGINE_ID"
    exit 0
+
+  elif [ "$VIASH_MODE" == "docker_image_id" ]; then
+    echo "$VIASH_DOCKER_IMAGE_ID"
+    exit 0
  
  # enter docker container
  elif [[ "$VIASH_MODE" == "debug" ]]; then
--- a/target/nextflow/concat_text/.config.vsh.yaml
+++ b/target/nextflow/concat_text/.config.vsh.yaml
@@ -170,15 +170,15 @@ build_info:
  engine: "docker|native"
  output: "target/nextflow/concat_text"
  executable: "target/nextflow/concat_text/main.nf"
-  viash_version: "0.9.0-RC6"
-  git_commit: "373be82129c13f50558c0dae25c07afe0866a8ba"
+  viash_version: "0.9.0-RC7"
+  git_commit: "5705b88fa20f267475b5d0ae1ca25dbf55ff1295"
  git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
  name: "craftbox"
  version: "main"
  description: "A collection of custom-tailored scripts and applied tools.\n"
  info: null
-  viash_version: "0.9.0-RC6"
+  viash_version: "0.9.0-RC7"
  source: "src"
  target: "target"
  config_mods:
--- a/target/nextflow/concat_text/main.nf
+++ b/target/nextflow/concat_text/main.nf
@@ -1,6 +1,6 @@
 // concat_text main
 // 
-// This wrapper script is auto-generated by viash 0.9.0-RC6 and is thus a
+// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
 // derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
 // Data Intuitive.
 // 
@@ -764,8 +764,11 @@ def runEach(Map args) {
  def fromState_ = args.fromState
  def toState_ = args.toState
  def filter_ = args.filter
+  def runIf_ = args.runIf
  def id_ = args.id

+  assert !runIf_ || runIf_ instanceof Closure: "runEach: must pass a Closure to runIf."
+
  workflow runEachWf {
    take: input_ch
    main:
@@ -787,7 +790,20 @@ def runEach(Map args) {
          [new_id] + tup.drop(1)
        }
        : filter_ch
-      def data_ch = id_ch | map{tup ->
+      def chPassthrough = null
+      def chRun = null
+      if (runIf_) {
+        def idRunIfBranch = id_ch.branch{ tup ->
+          run: runIf_(tup[0], tup[1], comp_)
+          passthrough: true
+        }
+        chPassthrough = idRunIfBranch.passthrough
+        chRun = idRunIfBranch.run
+      } else {
+        chRun = id_ch
+        chPassthrough = Channel.empty()
+      }
+      def data_ch = chRun | map{tup ->
          def new_data = tup[1]
          if (fromState_ instanceof Map) {
            new_data = fromState_.collectEntries{ key0, key1 ->
@@ -825,8 +841,11 @@ def runEach(Map args) {
          [tup[0], new_state] + tup.drop(3)
        }
        : out_ch
+
+      def return_ch = post_ch
+        | concat(chPassthrough)
      
-      post_ch
+      return_ch
    }

    // mix all results
@@ -1602,8 +1621,8 @@ def findStates(Map params, Map config) {
          // construct renameMap
          if (args.rename_keys) {
            def renameMap = args.rename_keys.collectEntries{renameString ->
-              def split = renameString.split(";")
-              assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey,newKey:oldKey'"
+              def split = renameString.split(":")
+              assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey', or 'newKey:oldKey;newKey:oldKey' in case of multiple values"
              split
            }

@@ -2630,30 +2649,31 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
        tuple
      }

-    def chModifiedFiltered = workflowArgs.filter ?
-      chModified | filter{workflowArgs.filter(it)} :
-      chModified

    def chRun = null
    def chPassthrough = null
    if (workflowArgs.runIf) {
-      def runIfBranch = chModifiedFiltered.branch{ tup ->
+      def runIfBranch = chModified.branch{ tup ->
        run: workflowArgs.runIf(tup[0], tup[1])
        passthrough: true
      }
      chRun = runIfBranch.run
      chPassthrough = runIfBranch.passthrough
    } else {
-      chRun = chModifiedFiltered
+      chRun = chModified
      chPassthrough = Channel.empty()
    }

+    def chRunFiltered = workflowArgs.filter ?
+      chRun | filter{workflowArgs.filter(it)} :
+      chRun
+
    def chArgs = workflowArgs.fromState ? 
-      chRun | map{
+      chRunFiltered | map{
        def new_data = workflowArgs.fromState(it.take(2))
        [it[0], new_data]
      } :
-      chRun | map {tup -> tup.take(2)}
+      chRunFiltered | map {tup -> tup.take(2)}

    // fill in defaults
    def chArgsWithDefaults = chArgs
@@ -2724,7 +2744,7 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
      // | view{"chInitialOutput: ${it.take(3)}"}

    // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chModifiedFiltered, key_)
+    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
      // input tuple format: [join_id, id, output, prev_state, ...]
      // output tuple format: [join_id, id, new_state, ...]
      | map{ tup ->
@@ -3004,15 +3024,15 @@ meta = [
    "runner" : "nextflow",
    "engine" : "docker|native",
    "output" : "target/nextflow/concat_text",
-    "viash_version" : "0.9.0-RC6",
-    "git_commit" : "373be82129c13f50558c0dae25c07afe0866a8ba",
+    "viash_version" : "0.9.0-RC7",
+    "git_commit" : "5705b88fa20f267475b5d0ae1ca25dbf55ff1295",
    "git_remote" : "https://github.com/viash-hub/craftbox"
  },
  "package_config" : {
    "name" : "craftbox",
    "version" : "main",
    "description" : "A collection of custom-tailored scripts and applied tools.\n",
-    "viash_version" : "0.9.0-RC6",
+    "viash_version" : "0.9.0-RC7",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
--- a/target/nextflow/concat_text/nextflow_schema.json
+++ b/target/nextflow/concat_text/nextflow_schema.json
@@ -17,8 +17,8 @@
                "input": {
                "type":
                "string",
-                "description": "Type: List of `file`, required, example: `input?.txt.gz`, multiple_sep: `\":\"`. A list of (gzipped) text files",
-                "help_text": "Type: List of `file`, required, example: `input?.txt.gz`, multiple_sep: `\":\"`. A list of (gzipped) text files."
+                "description": "Type: List of `file`, required, example: `input?.txt.gz`, multiple_sep: `\";\"`. A list of (gzipped) text files",
+                "help_text": "Type: List of `file`, required, example: `input?.txt.gz`, multiple_sep: `\";\"`. A list of (gzipped) text files."
            
            }
    
--- a/target/nextflow/csv2fasta/.config.vsh.yaml
+++ b/target/nextflow/csv2fasta/.config.vsh.yaml
@@ -221,15 +221,15 @@ build_info:
  engine: "docker|native"
  output: "target/nextflow/csv2fasta"
  executable: "target/nextflow/csv2fasta/main.nf"
-  viash_version: "0.9.0-RC6"
-  git_commit: "373be82129c13f50558c0dae25c07afe0866a8ba"
+  viash_version: "0.9.0-RC7"
+  git_commit: "5705b88fa20f267475b5d0ae1ca25dbf55ff1295"
  git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
  name: "craftbox"
  version: "main"
  description: "A collection of custom-tailored scripts and applied tools.\n"
  info: null
-  viash_version: "0.9.0-RC6"
+  viash_version: "0.9.0-RC7"
  source: "src"
  target: "target"
  config_mods:
--- a/target/nextflow/csv2fasta/main.nf
+++ b/target/nextflow/csv2fasta/main.nf
@@ -1,6 +1,6 @@
 // csv2fasta main
 // 
-// This wrapper script is auto-generated by viash 0.9.0-RC6 and is thus a
+// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
 // derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
 // Data Intuitive.
 // 
@@ -760,8 +760,11 @@ def runEach(Map args) {
  def fromState_ = args.fromState
  def toState_ = args.toState
  def filter_ = args.filter
+  def runIf_ = args.runIf
  def id_ = args.id

+  assert !runIf_ || runIf_ instanceof Closure: "runEach: must pass a Closure to runIf."
+
  workflow runEachWf {
    take: input_ch
    main:
@@ -783,7 +786,20 @@ def runEach(Map args) {
          [new_id] + tup.drop(1)
        }
        : filter_ch
-      def data_ch = id_ch | map{tup ->
+      def chPassthrough = null
+      def chRun = null
+      if (runIf_) {
+        def idRunIfBranch = id_ch.branch{ tup ->
+          run: runIf_(tup[0], tup[1], comp_)
+          passthrough: true
+        }
+        chPassthrough = idRunIfBranch.passthrough
+        chRun = idRunIfBranch.run
+      } else {
+        chRun = id_ch
+        chPassthrough = Channel.empty()
+      }
+      def data_ch = chRun | map{tup ->
          def new_data = tup[1]
          if (fromState_ instanceof Map) {
            new_data = fromState_.collectEntries{ key0, key1 ->
@@ -821,8 +837,11 @@ def runEach(Map args) {
          [tup[0], new_state] + tup.drop(3)
        }
        : out_ch
+
+      def return_ch = post_ch
+        | concat(chPassthrough)
      
-      post_ch
+      return_ch
    }

    // mix all results
@@ -1598,8 +1617,8 @@ def findStates(Map params, Map config) {
          // construct renameMap
          if (args.rename_keys) {
            def renameMap = args.rename_keys.collectEntries{renameString ->
-              def split = renameString.split(";")
-              assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey,newKey:oldKey'"
+              def split = renameString.split(":")
+              assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey', or 'newKey:oldKey;newKey:oldKey' in case of multiple values"
              split
            }

@@ -2626,30 +2645,31 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
        tuple
      }

-    def chModifiedFiltered = workflowArgs.filter ?
-      chModified | filter{workflowArgs.filter(it)} :
-      chModified

    def chRun = null
    def chPassthrough = null
    if (workflowArgs.runIf) {
-      def runIfBranch = chModifiedFiltered.branch{ tup ->
+      def runIfBranch = chModified.branch{ tup ->
        run: workflowArgs.runIf(tup[0], tup[1])
        passthrough: true
      }
      chRun = runIfBranch.run
      chPassthrough = runIfBranch.passthrough
    } else {
-      chRun = chModifiedFiltered
+      chRun = chModified
      chPassthrough = Channel.empty()
    }

+    def chRunFiltered = workflowArgs.filter ?
+      chRun | filter{workflowArgs.filter(it)} :
+      chRun
+
    def chArgs = workflowArgs.fromState ? 
-      chRun | map{
+      chRunFiltered | map{
        def new_data = workflowArgs.fromState(it.take(2))
        [it[0], new_data]
      } :
-      chRun | map {tup -> tup.take(2)}
+      chRunFiltered | map {tup -> tup.take(2)}

    // fill in defaults
    def chArgsWithDefaults = chArgs
@@ -2720,7 +2740,7 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
      // | view{"chInitialOutput: ${it.take(3)}"}

    // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chModifiedFiltered, key_)
+    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
      // input tuple format: [join_id, id, output, prev_state, ...]
      // output tuple format: [join_id, id, new_state, ...]
      | map{ tup ->
@@ -3040,15 +3060,15 @@ meta = [
    "runner" : "nextflow",
    "engine" : "docker|native",
    "output" : "target/nextflow/csv2fasta",
-    "viash_version" : "0.9.0-RC6",
-    "git_commit" : "373be82129c13f50558c0dae25c07afe0866a8ba",
+    "viash_version" : "0.9.0-RC7",
+    "git_commit" : "5705b88fa20f267475b5d0ae1ca25dbf55ff1295",
    "git_remote" : "https://github.com/viash-hub/craftbox"
  },
  "package_config" : {
    "name" : "craftbox",
    "version" : "main",
    "description" : "A collection of custom-tailored scripts and applied tools.\n",
-    "viash_version" : "0.9.0-RC6",
+    "viash_version" : "0.9.0-RC7",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
--- a/target/nextflow/untar/.config.vsh.yaml
+++ b/target/nextflow/untar/.config.vsh.yaml
@@ -146,15 +146,15 @@ build_info:
  engine: "docker|native"
  output: "target/nextflow/untar"
  executable: "target/nextflow/untar/main.nf"
-  viash_version: "0.9.0-RC6"
-  git_commit: "373be82129c13f50558c0dae25c07afe0866a8ba"
+  viash_version: "0.9.0-RC7"
+  git_commit: "5705b88fa20f267475b5d0ae1ca25dbf55ff1295"
  git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
  name: "craftbox"
  version: "main"
  description: "A collection of custom-tailored scripts and applied tools.\n"
  info: null
-  viash_version: "0.9.0-RC6"
+  viash_version: "0.9.0-RC7"
  source: "src"
  target: "target"
  config_mods:
--- a/target/nextflow/untar/main.nf
+++ b/target/nextflow/untar/main.nf
@@ -1,6 +1,6 @@
 // untar main
 // 
-// This wrapper script is auto-generated by viash 0.9.0-RC6 and is thus a
+// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
 // derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
 // Data Intuitive.
 // 
@@ -760,8 +760,11 @@ def runEach(Map args) {
  def fromState_ = args.fromState
  def toState_ = args.toState
  def filter_ = args.filter
+  def runIf_ = args.runIf
  def id_ = args.id

+  assert !runIf_ || runIf_ instanceof Closure: "runEach: must pass a Closure to runIf."
+
  workflow runEachWf {
    take: input_ch
    main:
@@ -783,7 +786,20 @@ def runEach(Map args) {
          [new_id] + tup.drop(1)
        }
        : filter_ch
-      def data_ch = id_ch | map{tup ->
+      def chPassthrough = null
+      def chRun = null
+      if (runIf_) {
+        def idRunIfBranch = id_ch.branch{ tup ->
+          run: runIf_(tup[0], tup[1], comp_)
+          passthrough: true
+        }
+        chPassthrough = idRunIfBranch.passthrough
+        chRun = idRunIfBranch.run
+      } else {
+        chRun = id_ch
+        chPassthrough = Channel.empty()
+      }
+      def data_ch = chRun | map{tup ->
          def new_data = tup[1]
          if (fromState_ instanceof Map) {
            new_data = fromState_.collectEntries{ key0, key1 ->
@@ -821,8 +837,11 @@ def runEach(Map args) {
          [tup[0], new_state] + tup.drop(3)
        }
        : out_ch
+
+      def return_ch = post_ch
+        | concat(chPassthrough)
      
-      post_ch
+      return_ch
    }

    // mix all results
@@ -1598,8 +1617,8 @@ def findStates(Map params, Map config) {
          // construct renameMap
          if (args.rename_keys) {
            def renameMap = args.rename_keys.collectEntries{renameString ->
-              def split = renameString.split(";")
-              assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey,newKey:oldKey'"
+              def split = renameString.split(":")
+              assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey', or 'newKey:oldKey;newKey:oldKey' in case of multiple values"
              split
            }

@@ -2626,30 +2645,31 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
        tuple
      }

-    def chModifiedFiltered = workflowArgs.filter ?
-      chModified | filter{workflowArgs.filter(it)} :
-      chModified

    def chRun = null
    def chPassthrough = null
    if (workflowArgs.runIf) {
-      def runIfBranch = chModifiedFiltered.branch{ tup ->
+      def runIfBranch = chModified.branch{ tup ->
        run: workflowArgs.runIf(tup[0], tup[1])
        passthrough: true
      }
      chRun = runIfBranch.run
      chPassthrough = runIfBranch.passthrough
    } else {
-      chRun = chModifiedFiltered
+      chRun = chModified
      chPassthrough = Channel.empty()
    }

+    def chRunFiltered = workflowArgs.filter ?
+      chRun | filter{workflowArgs.filter(it)} :
+      chRun
+
    def chArgs = workflowArgs.fromState ? 
-      chRun | map{
+      chRunFiltered | map{
        def new_data = workflowArgs.fromState(it.take(2))
        [it[0], new_data]
      } :
-      chRun | map {tup -> tup.take(2)}
+      chRunFiltered | map {tup -> tup.take(2)}

    // fill in defaults
    def chArgsWithDefaults = chArgs
@@ -2720,7 +2740,7 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
      // | view{"chInitialOutput: ${it.take(3)}"}

    // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chModifiedFiltered, key_)
+    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
      // input tuple format: [join_id, id, output, prev_state, ...]
      // output tuple format: [join_id, id, new_state, ...]
      | map{ tup ->
@@ -2961,15 +2981,15 @@ meta = [
    "runner" : "nextflow",
    "engine" : "docker|native",
    "output" : "target/nextflow/untar",
-    "viash_version" : "0.9.0-RC6",
-    "git_commit" : "373be82129c13f50558c0dae25c07afe0866a8ba",
+    "viash_version" : "0.9.0-RC7",
+    "git_commit" : "5705b88fa20f267475b5d0ae1ca25dbf55ff1295",
    "git_remote" : "https://github.com/viash-hub/craftbox"
  },
  "package_config" : {
    "name" : "craftbox",
    "version" : "main",
    "description" : "A collection of custom-tailored scripts and applied tools.\n",
-    "viash_version" : "0.9.0-RC6",
+    "viash_version" : "0.9.0-RC7",
    "source" : "src",
    "target" : "target",
    "config_mods" : [