Build branch main with version main (cfefb99)

Build pipeline: viash-hub.demultiplex.main-ks8mz Source commit: cfefb99ef0 Source message: Bump Viash version to 0.9.0
2024-09-12 12:30:59 +00:00
parent 54d722dcb7
commit 6c37efac8f
17 changed files with 393 additions and 192 deletions
--- a/_viash.yaml
+++ b/_viash.yaml
@@ -11,7 +11,7 @@ info:
    - path: https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz
      dest: test_resources

-viash_version: 0.9.0-RC6
+viash_version: 0.9.0

 config_mods: |
  .requirements.commands := ['ps']
--- a/target/executable/io/interop_summary_to_csv/.config.vsh.yaml
+++ b/target/executable/io/interop_summary_to_csv/.config.vsh.yaml
@@ -140,8 +140,8 @@ build_info:
  engine: "docker|native"
  output: "target/executable/io/interop_summary_to_csv"
  executable: "target/executable/io/interop_summary_to_csv/interop_summary_to_csv"
-  viash_version: "0.9.0-RC6"
-  git_commit: "ed860bed30c98b981270f104cffbdb9b7f1ce141"
+  viash_version: "0.9.0"
+  git_commit: "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f"
  git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
  name: "demultiplex"
@@ -151,7 +151,7 @@ package_config:
    test_resources:
    - path: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz"
      dest: "test_resources"
-  viash_version: "0.9.0-RC6"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/io/interop_summary_to_csv/interop_summary_to_csv
+++ b/target/executable/io/interop_summary_to_csv/interop_summary_to_csv
@@ -2,9 +2,9 @@

 # interop_summary_to_csv main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC6 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
+# Intuitive.
 # 
 # The component may contain files which fall under a different license. The
 # authors of this component should specify the license in the header of such
@@ -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
@@ -205,9 +205,9 @@ 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:"
@@ -259,9 +259,9 @@ 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."
@@ -281,7 +281,8 @@ 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 $1
    out=$?
@@ -305,9 +306,9 @@ 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 $@
@@ -469,9 +470,9 @@ 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="2024-06-24T12:46:52Z"
+LABEL org.opencontainers.image.created="2024-09-12T12:25:58Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="ed860bed30c98b981270f104cffbdb9b7f1ce141"
+LABEL org.opencontainers.image.revision="cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
@@ -498,6 +499,9 @@ function ViashDockerBuildArgs {
 #   ViashAbsolutePath /foo/bar/..     # returns /foo
 function ViashAbsolutePath {
  local thePath
+  local parr
+  local outp
+  local len
  if [[ ! "$1" =~ ^/ ]]; then
    thePath="$PWD/$1"
  else
@@ -531,11 +535,14 @@ function ViashAbsolutePath {
 # $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="$abs_path"
    base_name=""
@@ -543,7 +550,7 @@ function ViashDockerAutodetectMount {
    mount_source=`dirname "$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
@@ -551,7 +558,9 @@ 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="$abs_path"
    base_name=""
@@ -559,17 +568,22 @@ function ViashDockerAutodetectMountArg {
    mount_source=`dirname "$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)

@@ -653,6 +667,18 @@ 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 "$1")")
+            shift 1
+            ;;
+        ---docker_image_id)
+            VIASH_MODE='docker_image_id'
+            shift 1
+            ;;
        ---debug)
            VIASH_MODE='debug'
            shift 1
@@ -715,6 +741,10 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; 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
    VIASH_CMD="docker run --entrypoint=bash ${VIASH_DOCKER_RUN_ARGS[@]} -v '$(pwd)':/pwd --workdir /pwd -t $VIASH_DOCKER_IMAGE_ID"
--- a/target/executable/io/untar/.config.vsh.yaml
+++ b/target/executable/io/untar/.config.vsh.yaml
@@ -147,8 +147,8 @@ build_info:
  engine: "docker|native"
  output: "target/executable/io/untar"
  executable: "target/executable/io/untar/untar"
-  viash_version: "0.9.0-RC6"
-  git_commit: "ed860bed30c98b981270f104cffbdb9b7f1ce141"
+  viash_version: "0.9.0"
+  git_commit: "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f"
  git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
  name: "demultiplex"
@@ -158,7 +158,7 @@ package_config:
    test_resources:
    - path: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz"
      dest: "test_resources"
-  viash_version: "0.9.0-RC6"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/io/untar/untar
+++ b/target/executable/io/untar/untar
@@ -2,9 +2,9 @@

 # untar main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC6 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
+# Intuitive.
 # 
 # The component may contain files which fall under a different license. The
 # authors of this component should specify the license in the header of such
@@ -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 io untar"
-LABEL org.opencontainers.image.created="2024-06-24T12:46:53Z"
+LABEL org.opencontainers.image.created="2024-09-12T12:25:58Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="ed860bed30c98b981270f104cffbdb9b7f1ce141"
+LABEL org.opencontainers.image.revision="cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f"
 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
@@ -537,11 +541,14 @@ function ViashAbsolutePath {
 # $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 "$1")")
+            shift 1
+            ;;
+        ---docker_image_id)
+            VIASH_MODE='docker_image_id'
+            shift 1
+            ;;
        ---debug)
            VIASH_MODE='debug'
            shift 1
@@ -727,6 +753,10 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; 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
    VIASH_CMD="docker run --entrypoint=bash ${VIASH_DOCKER_RUN_ARGS[@]} -v '$(pwd)':/pwd --workdir /pwd -t $VIASH_DOCKER_IMAGE_ID"
--- a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml
+++ b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml
@@ -138,8 +138,8 @@ build_info:
  engine: "native|native"
  output: "target/nextflow/dataflow/combine_samples"
  executable: "target/nextflow/dataflow/combine_samples/main.nf"
-  viash_version: "0.9.0-RC6"
-  git_commit: "ed860bed30c98b981270f104cffbdb9b7f1ce141"
+  viash_version: "0.9.0"
+  git_commit: "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f"
  git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
  name: "demultiplex"
@@ -149,7 +149,7 @@ package_config:
    test_resources:
    - path: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz"
      dest: "test_resources"
-  viash_version: "0.9.0-RC6"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/nextflow/dataflow/combine_samples/main.nf
+++ b/target/nextflow/dataflow/combine_samples/main.nf
@@ -1,8 +1,8 @@
 // combine_samples main
 // 
-// This wrapper script is auto-generated by viash 0.9.0-RC6 and is thus a
-// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-// Data Intuitive.
+// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
+// Intuitive.
 // 
 // The component may contain files which fall under a different license. The
 // authors of this component should specify the license in the header of such
@@ -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 ->
@@ -822,7 +838,10 @@ def runEach(Map args) {
        }
        : out_ch

-      post_ch
+      def return_ch = post_ch
+        | concat(chPassthrough)
+      
+      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
            }

@@ -1709,7 +1728,9 @@ def publishStates(Map args) {

          def yamlFilename = yamlTemplate_
            .replaceAll('\\$id', id_)
+            .replaceAll('\\$\\{id\\}', id_)
            .replaceAll('\\$key', key_)
+            .replaceAll('\\$\\{key\\}', key_)

            // TODO: do the pathnames in state_ match up with the outputFilenames_?

@@ -1780,7 +1801,9 @@ def publishStatesByConfig(Map args) {
          def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml'
          def yamlFilename = yamlTemplate
            .replaceAll('\\$id', id_)
+            .replaceAll('\\$\\{id\\}', id_)
            .replaceAll('\\$key', key_)
+            .replaceAll('\\$\\{key\\}', key_)
          def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()

          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
@@ -1822,7 +1845,9 @@ def publishStatesByConfig(Map args) {
                // instantiate the template
                def filename = filenameTemplate
                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
                if (par.multiple) {
                  // if the parameter is multiple: true, the filename
                  // should contain a wildcard '*' that is replaced with
@@ -2626,30 +2651,31 @@ 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 +2746,7 @@ 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 ->
@@ -2945,8 +2971,8 @@ meta = [
    "runner" : "nextflow",
    "engine" : "native|native",
    "output" : "target/nextflow/dataflow/combine_samples",
-    "viash_version" : "0.9.0-RC6",
-    "git_commit" : "ed860bed30c98b981270f104cffbdb9b7f1ce141",
+    "viash_version" : "0.9.0",
+    "git_commit" : "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f",
    "git_remote" : "https://github.com/viash-hub/demultiplex"
  },
  "package_config" : {
@@ -2961,7 +2987,7 @@ meta = [
        }
      ]
    },
-    "viash_version" : "0.9.0-RC6",
+    "viash_version" : "0.9.0",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
--- a/target/nextflow/dataflow/combine_samples/nextflow_schema.json
+++ b/target/nextflow/dataflow/combine_samples/nextflow_schema.json
@@ -57,8 +57,8 @@
                "output_forward": {
                "type":
                "string",
-                "description": "Type: List of `file`, required, default: `$id.$key.output_forward_*.output_forward_*`, multiple_sep: `\":\"`. ",
-                "help_text": "Type: List of `file`, required, default: `$id.$key.output_forward_*.output_forward_*`, multiple_sep: `\":\"`. "
+                "description": "Type: List of `file`, required, default: `$id.$key.output_forward_*.output_forward_*`, multiple_sep: `\";\"`. ",
+                "help_text": "Type: List of `file`, required, default: `$id.$key.output_forward_*.output_forward_*`, multiple_sep: `\";\"`. "
            ,
                "default": "$id.$key.output_forward_*.output_forward_*"
            }
@@ -68,8 +68,8 @@
                "output_reverse": {
                "type":
                "string",
-                "description": "Type: List of `file`, default: `$id.$key.output_reverse_*.output_reverse_*`, multiple_sep: `\":\"`. ",
-                "help_text": "Type: List of `file`, default: `$id.$key.output_reverse_*.output_reverse_*`, multiple_sep: `\":\"`. "
+                "description": "Type: List of `file`, default: `$id.$key.output_reverse_*.output_reverse_*`, multiple_sep: `\";\"`. ",
+                "help_text": "Type: List of `file`, default: `$id.$key.output_reverse_*.output_reverse_*`, multiple_sep: `\";\"`. "
            ,
                "default": "$id.$key.output_reverse_*.output_reverse_*"
            }
--- a/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml
+++ b/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml
@@ -132,8 +132,8 @@ build_info:
  engine: "native|native"
  output: "target/nextflow/dataflow/gather_fastqs_and_validate"
  executable: "target/nextflow/dataflow/gather_fastqs_and_validate/main.nf"
-  viash_version: "0.9.0-RC6"
-  git_commit: "ed860bed30c98b981270f104cffbdb9b7f1ce141"
+  viash_version: "0.9.0"
+  git_commit: "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f"
  git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
  name: "demultiplex"
@@ -143,7 +143,7 @@ package_config:
    test_resources:
    - path: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz"
      dest: "test_resources"
-  viash_version: "0.9.0-RC6"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
+++ b/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
@@ -1,8 +1,8 @@
 // gather_fastqs_and_validate main
 // 
-// This wrapper script is auto-generated by viash 0.9.0-RC6 and is thus a
-// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-// Data Intuitive.
+// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
+// Intuitive.
 // 
 // The component may contain files which fall under a different license. The
 // authors of this component should specify the license in the header of such
@@ -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 ->
@@ -822,7 +838,10 @@ def runEach(Map args) {
        }
        : out_ch

-      post_ch
+      def return_ch = post_ch
+        | concat(chPassthrough)
+      
+      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
            }

@@ -1709,7 +1728,9 @@ def publishStates(Map args) {

          def yamlFilename = yamlTemplate_
            .replaceAll('\\$id', id_)
+            .replaceAll('\\$\\{id\\}', id_)
            .replaceAll('\\$key', key_)
+            .replaceAll('\\$\\{key\\}', key_)

            // TODO: do the pathnames in state_ match up with the outputFilenames_?

@@ -1780,7 +1801,9 @@ def publishStatesByConfig(Map args) {
          def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml'
          def yamlFilename = yamlTemplate
            .replaceAll('\\$id', id_)
+            .replaceAll('\\$\\{id\\}', id_)
            .replaceAll('\\$key', key_)
+            .replaceAll('\\$\\{key\\}', key_)
          def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()

          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
@@ -1822,7 +1845,9 @@ def publishStatesByConfig(Map args) {
                // instantiate the template
                def filename = filenameTemplate
                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
                if (par.multiple) {
                  // if the parameter is multiple: true, the filename
                  // should contain a wildcard '*' that is replaced with
@@ -2626,30 +2651,31 @@ 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 +2746,7 @@ 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 ->
@@ -2938,8 +2964,8 @@ meta = [
    "runner" : "nextflow",
    "engine" : "native|native",
    "output" : "target/nextflow/dataflow/gather_fastqs_and_validate",
-    "viash_version" : "0.9.0-RC6",
-    "git_commit" : "ed860bed30c98b981270f104cffbdb9b7f1ce141",
+    "viash_version" : "0.9.0",
+    "git_commit" : "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f",
    "git_remote" : "https://github.com/viash-hub/demultiplex"
  },
  "package_config" : {
@@ -2954,7 +2980,7 @@ meta = [
        }
      ]
    },
-    "viash_version" : "0.9.0-RC6",
+    "viash_version" : "0.9.0",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
--- a/target/nextflow/demultiplex/.config.vsh.yaml
+++ b/target/nextflow/demultiplex/.config.vsh.yaml
@@ -185,8 +185,8 @@ build_info:
  engine: "native|native"
  output: "target/nextflow/demultiplex"
  executable: "target/nextflow/demultiplex/main.nf"
-  viash_version: "0.9.0-RC6"
-  git_commit: "ed860bed30c98b981270f104cffbdb9b7f1ce141"
+  viash_version: "0.9.0"
+  git_commit: "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f"
  git_remote: "https://github.com/viash-hub/demultiplex"
  dependencies:
  - "target/nextflow/io/untar"
@@ -204,7 +204,7 @@ package_config:
    test_resources:
    - path: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz"
      dest: "test_resources"
-  viash_version: "0.9.0-RC6"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/nextflow/demultiplex/main.nf
+++ b/target/nextflow/demultiplex/main.nf
@@ -1,8 +1,8 @@
 // demultiplex main
 // 
-// This wrapper script is auto-generated by viash 0.9.0-RC6 and is thus a
-// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-// Data Intuitive.
+// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
+// Intuitive.
 // 
 // The component may contain files which fall under a different license. The
 // authors of this component should specify the license in the header of such
@@ -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 ->
@@ -822,7 +838,10 @@ def runEach(Map args) {
        }
        : out_ch

-      post_ch
+      def return_ch = post_ch
+        | concat(chPassthrough)
+      
+      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
            }

@@ -1709,7 +1728,9 @@ def publishStates(Map args) {

          def yamlFilename = yamlTemplate_
            .replaceAll('\\$id', id_)
+            .replaceAll('\\$\\{id\\}', id_)
            .replaceAll('\\$key', key_)
+            .replaceAll('\\$\\{key\\}', key_)

            // TODO: do the pathnames in state_ match up with the outputFilenames_?

@@ -1780,7 +1801,9 @@ def publishStatesByConfig(Map args) {
          def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml'
          def yamlFilename = yamlTemplate
            .replaceAll('\\$id', id_)
+            .replaceAll('\\$\\{id\\}', id_)
            .replaceAll('\\$key', key_)
+            .replaceAll('\\$\\{key\\}', key_)
          def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()

          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
@@ -1822,7 +1845,9 @@ def publishStatesByConfig(Map args) {
                // instantiate the template
                def filename = filenameTemplate
                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
                if (par.multiple) {
                  // if the parameter is multiple: true, the filename
                  // should contain a wildcard '*' that is replaced with
@@ -2626,30 +2651,31 @@ 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 +2746,7 @@ 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 ->
@@ -3022,8 +3048,8 @@ meta = [
    "runner" : "nextflow",
    "engine" : "native|native",
    "output" : "target/nextflow/demultiplex",
-    "viash_version" : "0.9.0-RC6",
-    "git_commit" : "ed860bed30c98b981270f104cffbdb9b7f1ce141",
+    "viash_version" : "0.9.0",
+    "git_commit" : "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f",
    "git_remote" : "https://github.com/viash-hub/demultiplex"
  },
  "package_config" : {
@@ -3038,7 +3064,7 @@ meta = [
        }
      ]
    },
-    "viash_version" : "0.9.0-RC6",
+    "viash_version" : "0.9.0",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
--- a/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml
+++ b/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml
@@ -140,8 +140,8 @@ build_info:
  engine: "docker|native"
  output: "target/nextflow/io/interop_summary_to_csv"
  executable: "target/nextflow/io/interop_summary_to_csv/main.nf"
-  viash_version: "0.9.0-RC6"
-  git_commit: "ed860bed30c98b981270f104cffbdb9b7f1ce141"
+  viash_version: "0.9.0"
+  git_commit: "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f"
  git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
  name: "demultiplex"
@@ -151,7 +151,7 @@ package_config:
    test_resources:
    - path: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz"
      dest: "test_resources"
-  viash_version: "0.9.0-RC6"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/nextflow/io/interop_summary_to_csv/main.nf
+++ b/target/nextflow/io/interop_summary_to_csv/main.nf
@@ -1,8 +1,8 @@
 // interop_summary_to_csv main
 // 
-// This wrapper script is auto-generated by viash 0.9.0-RC6 and is thus a
-// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-// Data Intuitive.
+// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
+// Intuitive.
 // 
 // The component may contain files which fall under a different license. The
 // authors of this component should specify the license in the header of such
@@ -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 ->
@@ -822,7 +838,10 @@ def runEach(Map args) {
        }
        : out_ch

-      post_ch
+      def return_ch = post_ch
+        | concat(chPassthrough)
+      
+      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
            }

@@ -1709,7 +1728,9 @@ def publishStates(Map args) {

          def yamlFilename = yamlTemplate_
            .replaceAll('\\$id', id_)
+            .replaceAll('\\$\\{id\\}', id_)
            .replaceAll('\\$key', key_)
+            .replaceAll('\\$\\{key\\}', key_)

            // TODO: do the pathnames in state_ match up with the outputFilenames_?

@@ -1780,7 +1801,9 @@ def publishStatesByConfig(Map args) {
          def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml'
          def yamlFilename = yamlTemplate
            .replaceAll('\\$id', id_)
+            .replaceAll('\\$\\{id\\}', id_)
            .replaceAll('\\$key', key_)
+            .replaceAll('\\$\\{key\\}', key_)
          def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()

          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
@@ -1822,7 +1845,9 @@ def publishStatesByConfig(Map args) {
                // instantiate the template
                def filename = filenameTemplate
                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
                if (par.multiple) {
                  // if the parameter is multiple: true, the filename
                  // should contain a wildcard '*' that is replaced with
@@ -2626,30 +2651,31 @@ 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 +2746,7 @@ 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 ->
@@ -2950,8 +2976,8 @@ meta = [
    "runner" : "nextflow",
    "engine" : "docker|native",
    "output" : "target/nextflow/io/interop_summary_to_csv",
-    "viash_version" : "0.9.0-RC6",
-    "git_commit" : "ed860bed30c98b981270f104cffbdb9b7f1ce141",
+    "viash_version" : "0.9.0",
+    "git_commit" : "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f",
    "git_remote" : "https://github.com/viash-hub/demultiplex"
  },
  "package_config" : {
@@ -2966,7 +2992,7 @@ meta = [
        }
      ]
    },
-    "viash_version" : "0.9.0-RC6",
+    "viash_version" : "0.9.0",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
@@ -3115,7 +3141,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) {
              val = val.join(par.multiple_sep)
            }
            if (par.direction == "output" && par.type == "file") {
-              val = val.replaceAll('\\$id', id).replaceAll('\\$key', key)
+              val = val
+                .replaceAll('\\$id', id)
+                .replaceAll('\\$\\{id\\}', id)
+                .replaceAll('\\$key', key)
+                .replaceAll('\\$\\{key\\}', key)
            }
            [parName, val]
          }
@@ -3246,7 +3276,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  def createParentStr = meta.config.allArguments
    .findAll { it.type == "file" && it.direction == "output" && it.create_parent }
    .collect { par -> 
-      "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }"
+      def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]"
+      "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }"
    }
    .join("\n")

@@ -3254,8 +3285,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  def inputFileExports = meta.config.allArguments
    .findAll { it.type == "file" && it.direction.toLowerCase() == "input" }
    .collect { par ->
-      def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})"
-      "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}"
+      def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}"
+      "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}"
    }

  // NOTE: if using docker, use /tmp instead of tmpDir!
@@ -3292,6 +3323,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  def procStr = 
  """nextflow.enable.dsl=2
  |
+  |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") }
  |process $procKey {$drctvStrs
  |input:
  |  tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources")
@@ -3303,10 +3335,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  |$stub
  |\"\"\"
  |script:$assertStr
-  |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') }
  |def parInject = args
  |  .findAll{key, value -> value != null}
-  |  .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""}
+  |  .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"}
  |  .join("\\n")
  |\"\"\"
  |# meta exports
--- a/target/nextflow/io/untar/.config.vsh.yaml
+++ b/target/nextflow/io/untar/.config.vsh.yaml
@@ -147,8 +147,8 @@ build_info:
  engine: "docker|native"
  output: "target/nextflow/io/untar"
  executable: "target/nextflow/io/untar/main.nf"
-  viash_version: "0.9.0-RC6"
-  git_commit: "ed860bed30c98b981270f104cffbdb9b7f1ce141"
+  viash_version: "0.9.0"
+  git_commit: "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f"
  git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
  name: "demultiplex"
@@ -158,7 +158,7 @@ package_config:
    test_resources:
    - path: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz"
      dest: "test_resources"
-  viash_version: "0.9.0-RC6"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/nextflow/io/untar/main.nf
+++ b/target/nextflow/io/untar/main.nf
@@ -1,8 +1,8 @@
 // untar main
 // 
-// This wrapper script is auto-generated by viash 0.9.0-RC6 and is thus a
-// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-// Data Intuitive.
+// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
+// Intuitive.
 // 
 // The component may contain files which fall under a different license. The
 // authors of this component should specify the license in the header of such
@@ -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 ->
@@ -822,7 +838,10 @@ def runEach(Map args) {
        }
        : out_ch

-      post_ch
+      def return_ch = post_ch
+        | concat(chPassthrough)
+      
+      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
            }

@@ -1709,7 +1728,9 @@ def publishStates(Map args) {

          def yamlFilename = yamlTemplate_
            .replaceAll('\\$id', id_)
+            .replaceAll('\\$\\{id\\}', id_)
            .replaceAll('\\$key', key_)
+            .replaceAll('\\$\\{key\\}', key_)

            // TODO: do the pathnames in state_ match up with the outputFilenames_?

@@ -1780,7 +1801,9 @@ def publishStatesByConfig(Map args) {
          def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml'
          def yamlFilename = yamlTemplate
            .replaceAll('\\$id', id_)
+            .replaceAll('\\$\\{id\\}', id_)
            .replaceAll('\\$key', key_)
+            .replaceAll('\\$\\{key\\}', key_)
          def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()

          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
@@ -1822,7 +1845,9 @@ def publishStatesByConfig(Map args) {
                // instantiate the template
                def filename = filenameTemplate
                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
                if (par.multiple) {
                  // if the parameter is multiple: true, the filename
                  // should contain a wildcard '*' that is replaced with
@@ -2626,30 +2651,31 @@ 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 +2746,7 @@ 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 ->
@@ -2962,8 +2988,8 @@ meta = [
    "runner" : "nextflow",
    "engine" : "docker|native",
    "output" : "target/nextflow/io/untar",
-    "viash_version" : "0.9.0-RC6",
-    "git_commit" : "ed860bed30c98b981270f104cffbdb9b7f1ce141",
+    "viash_version" : "0.9.0",
+    "git_commit" : "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f",
    "git_remote" : "https://github.com/viash-hub/demultiplex"
  },
  "package_config" : {
@@ -2978,7 +3004,7 @@ meta = [
        }
      ]
    },
-    "viash_version" : "0.9.0-RC6",
+    "viash_version" : "0.9.0",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
@@ -3157,7 +3183,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) {
              val = val.join(par.multiple_sep)
            }
            if (par.direction == "output" && par.type == "file") {
-              val = val.replaceAll('\\$id', id).replaceAll('\\$key', key)
+              val = val
+                .replaceAll('\\$id', id)
+                .replaceAll('\\$\\{id\\}', id)
+                .replaceAll('\\$key', key)
+                .replaceAll('\\$\\{key\\}', key)
            }
            [parName, val]
          }
@@ -3288,7 +3318,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  def createParentStr = meta.config.allArguments
    .findAll { it.type == "file" && it.direction == "output" && it.create_parent }
    .collect { par -> 
-      "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }"
+      def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]"
+      "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }"
    }
    .join("\n")

@@ -3296,8 +3327,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  def inputFileExports = meta.config.allArguments
    .findAll { it.type == "file" && it.direction.toLowerCase() == "input" }
    .collect { par ->
-      def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})"
-      "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}"
+      def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}"
+      "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}"
    }

  // NOTE: if using docker, use /tmp instead of tmpDir!
@@ -3334,6 +3365,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  def procStr = 
  """nextflow.enable.dsl=2
  |
+  |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") }
  |process $procKey {$drctvStrs
  |input:
  |  tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources")
@@ -3345,10 +3377,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  |$stub
  |\"\"\"
  |script:$assertStr
-  |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') }
  |def parInject = args
  |  .findAll{key, value -> value != null}
-  |  .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""}
+  |  .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"}
  |  .join("\\n")
  |\"\"\"
  |# meta exports
--- a/1
+++ b/1
@@ -0,0 +1 @@
+/work/viash_hub_resources/viash-hub/demultiplex/ebb861b02ab66db004c32fa46573bb1e/200624_A00834_0183_BHMTFYDRXX.tar.gz
				`@@ -0,0 +1 @@`
				`/work/viash_hub_resources/viash-hub/demultiplex/ebb861b02ab66db004c32fa46573bb1e/200624_A00834_0183_BHMTFYDRXX.tar.gz`