From 5d74ec3308b2f086db7fc968c6b247641792be01 Mon Sep 17 00:00:00 2001
From: CI <toni@data-intuitive.com>
Date: Thu, 12 Sep 2024 15:52:47 +0000
Subject: [PATCH] Build branch v0.1 with version v0.1.1 (ff28cec)

Build pipeline: viash-hub.demultiplex.v0.1-79dfz

Source commit: https://github.com/viash-hub/demultiplex/commit/ff28cec6bd0ff4f8e52c6b2cf0c9cc990cf20add

Source message: Merge main and fix conflicts
---
 _viash.yaml                                   |   4 +-
 nextflow.config                               |   2 +-
 .../interop_summary_to_csv/.config.vsh.yaml   |  14 +--
 .../interop_summary_to_csv                    | 104 +++++++++++-------
 target/executable/io/untar/.config.vsh.yaml   |  14 +--
 target/executable/io/untar/untar              | 104 +++++++++++-------
 .../dataflow/combine_samples/.config.vsh.yaml |  12 +-
 .../nextflow/dataflow/combine_samples/main.nf |  70 ++++++++----
 .../dataflow/combine_samples/nextflow.config  |   2 +-
 .../combine_samples/nextflow_schema.json      |   8 +-
 .../.config.vsh.yaml                          |  12 +-
 .../gather_fastqs_and_validate/main.nf        |  70 ++++++++----
 .../nextflow.config                           |   2 +-
 target/nextflow/demultiplex/.config.vsh.yaml  |  12 +-
 target/nextflow/demultiplex/main.nf           |  70 ++++++++----
 target/nextflow/demultiplex/nextflow.config   |   2 +-
 .../interop_summary_to_csv/.config.vsh.yaml   |  14 +--
 .../io/interop_summary_to_csv/main.nf         |  91 ++++++++++-----
 .../io/interop_summary_to_csv/nextflow.config |   2 +-
 target/nextflow/io/untar/.config.vsh.yaml     |  14 +--
 target/nextflow/io/untar/main.nf              |  91 ++++++++++-----
 target/nextflow/io/untar/nextflow.config      |   2 +-
 test_resources                                |   1 +
 23 files changed, 459 insertions(+), 258 deletions(-)
 create mode 120000 test_resources

diff --git a/_viash.yaml b/_viash.yaml
index 24b920c..523fcb6 100644
--- a/_viash.yaml
+++ b/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.1.0
+version: v0.1.1
 description: |
   Demultiplexing pipeline
 license: MIT
@@ -12,7 +12,7 @@ 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']
diff --git a/nextflow.config b/nextflow.config
index 137d6e2..ade3a48 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -1,6 +1,6 @@
 manifest {
   name = "demultiplex"
-  version = "v0.1.0"
+  version = "v0.1.1"
   defaultBranch = "main"
   nextflowVersion = "!>=20.12.1-edge"
 }
diff --git a/target/executable/io/interop_summary_to_csv/.config.vsh.yaml b/target/executable/io/interop_summary_to_csv/.config.vsh.yaml
index 42f3b90..4069227 100644
--- a/target/executable/io/interop_summary_to_csv/.config.vsh.yaml
+++ b/target/executable/io/interop_summary_to_csv/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "interop_summary_to_csv"
 namespace: "io"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -116,7 +116,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -140,25 +140,25 @@ 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: "3d229bef584233f228330ff881dad685b92bf1e1"
+  viash_version: "0.9.0"
+  git_commit: "ff28cec6bd0ff4f8e52c6b2cf0c9cc990cf20add"
   git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
   name: "demultiplex"
-  version: "v0.1.0"
+  version: "v0.1.1"
   description: "Demultiplexing pipeline\n"
   info:
     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:
   - ".requirements.commands := ['ps']\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
   keywords:
   - "bioinformatics"
   - "sequence"
diff --git a/target/executable/io/interop_summary_to_csv/interop_summary_to_csv b/target/executable/io/interop_summary_to_csv/interop_summary_to_csv
index 458947f..3ab3b4b 100755
--- a/target/executable/io/interop_summary_to_csv/interop_summary_to_csv
+++ b/target/executable/io/interop_summary_to_csv/interop_summary_to_csv
@@ -1,10 +1,10 @@
 #!/usr/bin/env bash
 
-# interop_summary_to_csv v0.1.0
+# interop_summary_to_csv v0.1.1
 # 
-# 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 $source
 }
 # see https://en.wikipedia.org/wiki/Syslog#Severity_level
 VIASH_LOGCODE_EMERGENCY=0
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "interop_summary_to_csv v0.1.0"
+  echo "interop_summary_to_csv v0.1.1"
   echo ""
   echo "Input arguments:"
   echo "    --input"
@@ -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 $@
@@ -469,10 +470,10 @@ tar -C /tmp/ --no-same-owner --no-same-permissions -xvf /tmp/interop.tar.gz && \
 mv /tmp/interop-1.3.1-Linux-GNU/bin/index-summary /tmp/interop-1.3.1-Linux-GNU/bin/summary /usr/local/bin/
 
 LABEL org.opencontainers.image.description="Companion container for running component io interop_summary_to_csv"
-LABEL org.opencontainers.image.created="2024-06-24T12:57:03Z"
+LABEL org.opencontainers.image.created="2024-09-12T15:46:50Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="3d229bef584233f228330ff881dad685b92bf1e1"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.revision="ff28cec6bd0ff4f8e52c6b2cf0c9cc990cf20add"
+LABEL org.opencontainers.image.version="v0.1.1"
 
 VIASHDOCKER
   fi
@@ -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
@@ -528,14 +532,17 @@ 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="$abs_path"
     base_name=""
@@ -543,7 +550,7 @@ function ViashDockerAutodetectMount {
     mount_source=`dirname "$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)
 
@@ -595,7 +609,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "interop_summary_to_csv v0.1.0"
+            echo "interop_summary_to_csv v0.1.1"
             exit
             ;;
         --input)
@@ -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 "$1")")
+            shift 1
+            ;;
+        ---docker_image_id)
+            VIASH_MODE='docker_image_id'
+            shift 1
+            ;;
         ---debug)
             VIASH_MODE='debug'
             shift 1
@@ -707,13 +733,17 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/interop_summary_to_csv:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/interop_summary_to_csv:v0.1.1'
   fi
 
   # print dockerfile
   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
diff --git a/target/executable/io/untar/.config.vsh.yaml b/target/executable/io/untar/.config.vsh.yaml
index e2de2ca..5394451 100644
--- a/target/executable/io/untar/.config.vsh.yaml
+++ b/target/executable/io/untar/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "untar"
 namespace: "io"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -130,7 +130,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -147,25 +147,25 @@ build_info:
   engine: "docker|native"
   output: "target/executable/io/untar"
   executable: "target/executable/io/untar/untar"
-  viash_version: "0.9.0-RC6"
-  git_commit: "3d229bef584233f228330ff881dad685b92bf1e1"
+  viash_version: "0.9.0"
+  git_commit: "ff28cec6bd0ff4f8e52c6b2cf0c9cc990cf20add"
   git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
   name: "demultiplex"
-  version: "v0.1.0"
+  version: "v0.1.1"
   description: "Demultiplexing pipeline\n"
   info:
     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:
   - ".requirements.commands := ['ps']\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
   keywords:
   - "bioinformatics"
   - "sequence"
diff --git a/target/executable/io/untar/untar b/target/executable/io/untar/untar
index 4db2d58..92877e4 100755
--- a/target/executable/io/untar/untar
+++ b/target/executable/io/untar/untar
@@ -1,10 +1,10 @@
 #!/usr/bin/env bash
 
-# untar v0.1.0
+# untar v0.1.1
 # 
-# 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 $source
 }
 # see https://en.wikipedia.org/wiki/Syslog#Severity_level
 VIASH_LOGCODE_EMERGENCY=0
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "untar v0.1.0"
+  echo "untar v0.1.1"
   echo ""
   echo "Unpack a .tar file. When the contents of the .tar file is just a single"
   echo "directory,"
@@ -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 $@
@@ -475,10 +476,10 @@ RUN apt-get update && \
   rm -rf /var/lib/apt/lists/*
 
 LABEL org.opencontainers.image.description="Companion container for running component io untar"
-LABEL org.opencontainers.image.created="2024-06-24T12:57:03Z"
+LABEL org.opencontainers.image.created="2024-09-12T15:46:50Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="3d229bef584233f228330ff881dad685b92bf1e1"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.revision="ff28cec6bd0ff4f8e52c6b2cf0c9cc990cf20add"
+LABEL org.opencontainers.image.version="v0.1.1"
 
 VIASHDOCKER
   fi
@@ -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)
 
@@ -601,7 +615,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "untar v0.1.0"
+            echo "untar v0.1.1"
             exit
             ;;
         --input)
@@ -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 "$1")")
+            shift 1
+            ;;
+        ---docker_image_id)
+            VIASH_MODE='docker_image_id'
+            shift 1
+            ;;
         ---debug)
             VIASH_MODE='debug'
             shift 1
@@ -719,13 +745,17 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/untar:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/untar:v0.1.1'
   fi
 
   # print dockerfile
   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
diff --git a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml
index e511a40..d424b5c 100644
--- a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml
+++ b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "combine_samples"
 namespace: "dataflow"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -138,25 +138,25 @@ 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: "3d229bef584233f228330ff881dad685b92bf1e1"
+  viash_version: "0.9.0"
+  git_commit: "ff28cec6bd0ff4f8e52c6b2cf0c9cc990cf20add"
   git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
   name: "demultiplex"
-  version: "v0.1.0"
+  version: "v0.1.1"
   description: "Demultiplexing pipeline\n"
   info:
     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:
   - ".requirements.commands := ['ps']\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
   keywords:
   - "bioinformatics"
   - "sequence"
diff --git a/target/nextflow/dataflow/combine_samples/main.nf b/target/nextflow/dataflow/combine_samples/main.nf
index 76581c9..dc6b51e 100644
--- a/target/nextflow/dataflow/combine_samples/main.nf
+++ b/target/nextflow/dataflow/combine_samples/main.nf
@@ -1,8 +1,8 @@
-// combine_samples v0.1.0
+// combine_samples v0.1.1
 // 
-// 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 ->
@@ -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
             }
 
@@ -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 ->
@@ -2780,7 +2806,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "combine_samples",
   "namespace" : "dataflow",
-  "version" : "v0.1.0",
+  "version" : "v0.1.1",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -2945,13 +2971,13 @@ meta = [
     "runner" : "nextflow",
     "engine" : "native|native",
     "output" : "target/nextflow/dataflow/combine_samples",
-    "viash_version" : "0.9.0-RC6",
-    "git_commit" : "3d229bef584233f228330ff881dad685b92bf1e1",
+    "viash_version" : "0.9.0",
+    "git_commit" : "ff28cec6bd0ff4f8e52c6b2cf0c9cc990cf20add",
     "git_remote" : "https://github.com/viash-hub/demultiplex"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.1.0",
+    "version" : "v0.1.1",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -2961,14 +2987,14 @@ meta = [
         }
       ]
     },
-    "viash_version" : "0.9.0-RC6",
+    "viash_version" : "0.9.0",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
       ".requirements.commands := ['ps']\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
     ],
     "keywords" : [
       "bioinformatics",
diff --git a/target/nextflow/dataflow/combine_samples/nextflow.config b/target/nextflow/dataflow/combine_samples/nextflow.config
index 9b2304b..0c1afc1 100644
--- a/target/nextflow/dataflow/combine_samples/nextflow.config
+++ b/target/nextflow/dataflow/combine_samples/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'dataflow/combine_samples'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.1.0'
+  version = 'v0.1.1'
   description = 'Combine fastq files from across samples into one event with a list of fastq files per orientation.'
 }
 
diff --git a/target/nextflow/dataflow/combine_samples/nextflow_schema.json b/target/nextflow/dataflow/combine_samples/nextflow_schema.json
index a927314..245efb4 100644
--- 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_*"
             }
diff --git a/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml b/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml
index 6574b49..df6678b 100644
--- a/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml
+++ b/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "gather_fastqs_and_validate"
 namespace: "dataflow"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -132,25 +132,25 @@ 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: "3d229bef584233f228330ff881dad685b92bf1e1"
+  viash_version: "0.9.0"
+  git_commit: "ff28cec6bd0ff4f8e52c6b2cf0c9cc990cf20add"
   git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
   name: "demultiplex"
-  version: "v0.1.0"
+  version: "v0.1.1"
   description: "Demultiplexing pipeline\n"
   info:
     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:
   - ".requirements.commands := ['ps']\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
   keywords:
   - "bioinformatics"
   - "sequence"
diff --git a/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf b/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
index 21d740f..6246895 100644
--- 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 v0.1.0
+// gather_fastqs_and_validate v0.1.1
 // 
-// 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 ->
@@ -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
             }
 
@@ -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 ->
@@ -2780,7 +2806,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "gather_fastqs_and_validate",
   "namespace" : "dataflow",
-  "version" : "v0.1.0",
+  "version" : "v0.1.1",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -2938,13 +2964,13 @@ meta = [
     "runner" : "nextflow",
     "engine" : "native|native",
     "output" : "target/nextflow/dataflow/gather_fastqs_and_validate",
-    "viash_version" : "0.9.0-RC6",
-    "git_commit" : "3d229bef584233f228330ff881dad685b92bf1e1",
+    "viash_version" : "0.9.0",
+    "git_commit" : "ff28cec6bd0ff4f8e52c6b2cf0c9cc990cf20add",
     "git_remote" : "https://github.com/viash-hub/demultiplex"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.1.0",
+    "version" : "v0.1.1",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -2954,14 +2980,14 @@ meta = [
         }
       ]
     },
-    "viash_version" : "0.9.0-RC6",
+    "viash_version" : "0.9.0",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
       ".requirements.commands := ['ps']\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
     ],
     "keywords" : [
       "bioinformatics",
diff --git a/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow.config b/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow.config
index bb57715..256c85d 100644
--- a/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow.config
+++ b/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'dataflow/gather_fastqs_and_validate'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.1.0'
+  version = 'v0.1.1'
   description = 'From a directory containing fastq files, gather the files per sample \nand validate according to the contents of the sample sheet.\n'
 }
 
diff --git a/target/nextflow/demultiplex/.config.vsh.yaml b/target/nextflow/demultiplex/.config.vsh.yaml
index b41ec74..e2b958b 100644
--- a/target/nextflow/demultiplex/.config.vsh.yaml
+++ b/target/nextflow/demultiplex/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "demultiplex"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -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: "3d229bef584233f228330ff881dad685b92bf1e1"
+  viash_version: "0.9.0"
+  git_commit: "ff28cec6bd0ff4f8e52c6b2cf0c9cc990cf20add"
   git_remote: "https://github.com/viash-hub/demultiplex"
   dependencies:
   - "target/nextflow/io/untar"
@@ -198,20 +198,20 @@ build_info:
   - "target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/multiqc"
 package_config:
   name: "demultiplex"
-  version: "v0.1.0"
+  version: "v0.1.1"
   description: "Demultiplexing pipeline\n"
   info:
     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:
   - ".requirements.commands := ['ps']\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
   keywords:
   - "bioinformatics"
   - "sequence"
diff --git a/target/nextflow/demultiplex/main.nf b/target/nextflow/demultiplex/main.nf
index 44848bb..364faf5 100644
--- a/target/nextflow/demultiplex/main.nf
+++ b/target/nextflow/demultiplex/main.nf
@@ -1,8 +1,8 @@
-// demultiplex v0.1.0
+// demultiplex v0.1.1
 // 
-// 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 ->
@@ -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
             }
 
@@ -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 ->
@@ -2779,7 +2805,7 @@ meta = [
   "resources_dir": moduleDir.toRealPath().normalize(),
   "config": processConfig(readJsonBlob('''{
   "name" : "demultiplex",
-  "version" : "v0.1.0",
+  "version" : "v0.1.1",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -3022,13 +3048,13 @@ meta = [
     "runner" : "nextflow",
     "engine" : "native|native",
     "output" : "target/nextflow/demultiplex",
-    "viash_version" : "0.9.0-RC6",
-    "git_commit" : "3d229bef584233f228330ff881dad685b92bf1e1",
+    "viash_version" : "0.9.0",
+    "git_commit" : "ff28cec6bd0ff4f8e52c6b2cf0c9cc990cf20add",
     "git_remote" : "https://github.com/viash-hub/demultiplex"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.1.0",
+    "version" : "v0.1.1",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -3038,14 +3064,14 @@ meta = [
         }
       ]
     },
-    "viash_version" : "0.9.0-RC6",
+    "viash_version" : "0.9.0",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
       ".requirements.commands := ['ps']\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
     ],
     "keywords" : [
       "bioinformatics",
diff --git a/target/nextflow/demultiplex/nextflow.config b/target/nextflow/demultiplex/nextflow.config
index 6985af3..6a2a01e 100644
--- a/target/nextflow/demultiplex/nextflow.config
+++ b/target/nextflow/demultiplex/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'demultiplex'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.1.0'
+  version = 'v0.1.1'
   description = 'Demultiplexing of raw sequencing data'
 }
 
diff --git a/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml b/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml
index 740b5cd..e177c45 100644
--- a/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml
+++ b/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "interop_summary_to_csv"
 namespace: "io"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -116,7 +116,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -140,25 +140,25 @@ 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: "3d229bef584233f228330ff881dad685b92bf1e1"
+  viash_version: "0.9.0"
+  git_commit: "ff28cec6bd0ff4f8e52c6b2cf0c9cc990cf20add"
   git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
   name: "demultiplex"
-  version: "v0.1.0"
+  version: "v0.1.1"
   description: "Demultiplexing pipeline\n"
   info:
     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:
   - ".requirements.commands := ['ps']\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
   keywords:
   - "bioinformatics"
   - "sequence"
diff --git a/target/nextflow/io/interop_summary_to_csv/main.nf b/target/nextflow/io/interop_summary_to_csv/main.nf
index 7c7e752..d508f84 100644
--- 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 v0.1.0
+// interop_summary_to_csv v0.1.1
 // 
-// 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 ->
@@ -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
             }
 
@@ -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 ->
@@ -2780,7 +2806,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "interop_summary_to_csv",
   "namespace" : "io",
-  "version" : "v0.1.0",
+  "version" : "v0.1.1",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -2921,7 +2947,7 @@ meta = [
       "id" : "docker",
       "image" : "debian:stable-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.1.0",
+      "target_tag" : "v0.1.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -2950,13 +2976,13 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/io/interop_summary_to_csv",
-    "viash_version" : "0.9.0-RC6",
-    "git_commit" : "3d229bef584233f228330ff881dad685b92bf1e1",
+    "viash_version" : "0.9.0",
+    "git_commit" : "ff28cec6bd0ff4f8e52c6b2cf0c9cc990cf20add",
     "git_remote" : "https://github.com/viash-hub/demultiplex"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.1.0",
+    "version" : "v0.1.1",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -2966,14 +2992,14 @@ meta = [
         }
       ]
     },
-    "viash_version" : "0.9.0-RC6",
+    "viash_version" : "0.9.0",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
       ".requirements.commands := ['ps']\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -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:$assertStr
-  |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') }
   |def parInject = args
   |  .findAll{key, value -> value != null}
-  |  .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""}
+  |  .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"}
   |  .join("\\n")
   |\"\"\"
   |# meta exports
@@ -3391,7 +3422,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/demultiplex/io/interop_summary_to_csv",
-    "tag" : "v0.1.0"
+    "tag" : "v0.1.1"
   },
   "tag" : "$id"
 }'''),
diff --git a/target/nextflow/io/interop_summary_to_csv/nextflow.config b/target/nextflow/io/interop_summary_to_csv/nextflow.config
index 40d040c..096b85d 100644
--- a/target/nextflow/io/interop_summary_to_csv/nextflow.config
+++ b/target/nextflow/io/interop_summary_to_csv/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'io/interop_summary_to_csv'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.1.0'
+  version = 'v0.1.1'
 }
 
 process.container = 'nextflow/bash:latest'
diff --git a/target/nextflow/io/untar/.config.vsh.yaml b/target/nextflow/io/untar/.config.vsh.yaml
index d09489c..20cc161 100644
--- a/target/nextflow/io/untar/.config.vsh.yaml
+++ b/target/nextflow/io/untar/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "untar"
 namespace: "io"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -130,7 +130,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -147,25 +147,25 @@ 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: "3d229bef584233f228330ff881dad685b92bf1e1"
+  viash_version: "0.9.0"
+  git_commit: "ff28cec6bd0ff4f8e52c6b2cf0c9cc990cf20add"
   git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
   name: "demultiplex"
-  version: "v0.1.0"
+  version: "v0.1.1"
   description: "Demultiplexing pipeline\n"
   info:
     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:
   - ".requirements.commands := ['ps']\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
   keywords:
   - "bioinformatics"
   - "sequence"
diff --git a/target/nextflow/io/untar/main.nf b/target/nextflow/io/untar/main.nf
index 6e30cdc..38749c3 100644
--- a/target/nextflow/io/untar/main.nf
+++ b/target/nextflow/io/untar/main.nf
@@ -1,8 +1,8 @@
-// untar v0.1.0
+// untar v0.1.1
 // 
-// 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 ->
@@ -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
             }
 
@@ -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 ->
@@ -2780,7 +2806,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "untar",
   "namespace" : "io",
-  "version" : "v0.1.0",
+  "version" : "v0.1.1",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -2940,7 +2966,7 @@ meta = [
       "id" : "docker",
       "image" : "debian:stable-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.1.0",
+      "target_tag" : "v0.1.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -2962,13 +2988,13 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/io/untar",
-    "viash_version" : "0.9.0-RC6",
-    "git_commit" : "3d229bef584233f228330ff881dad685b92bf1e1",
+    "viash_version" : "0.9.0",
+    "git_commit" : "ff28cec6bd0ff4f8e52c6b2cf0c9cc990cf20add",
     "git_remote" : "https://github.com/viash-hub/demultiplex"
   },
   "package_config" : {
     "name" : "demultiplex",
-    "version" : "v0.1.0",
+    "version" : "v0.1.1",
     "description" : "Demultiplexing pipeline\n",
     "info" : {
       "test_resources" : [
@@ -2978,14 +3004,14 @@ meta = [
         }
       ]
     },
-    "viash_version" : "0.9.0-RC6",
+    "viash_version" : "0.9.0",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
       ".requirements.commands := ['ps']\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -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:$assertStr
-  |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') }
   |def parInject = args
   |  .findAll{key, value -> value != null}
-  |  .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""}
+  |  .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"}
   |  .join("\\n")
   |\"\"\"
   |# meta exports
@@ -3433,7 +3464,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/demultiplex/io/untar",
-    "tag" : "v0.1.0"
+    "tag" : "v0.1.1"
   },
   "tag" : "$id"
 }'''),
diff --git a/target/nextflow/io/untar/nextflow.config b/target/nextflow/io/untar/nextflow.config
index 468dfb4..71336eb 100644
--- a/target/nextflow/io/untar/nextflow.config
+++ b/target/nextflow/io/untar/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'io/untar'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.1.0'
+  version = 'v0.1.1'
   description = 'Unpack a .tar file. When the contents of the .tar file is just a single directory,\nput the contents of the directory into the output folder instead of that directory.\n'
 }
 
diff --git a/test_resources b/test_resources
new file mode 120000
index 0000000..6970768
--- /dev/null
+++ b/test_resources
@@ -0,0 +1 @@
+/work/viash_hub_resources/viash-hub/demultiplex/ebb861b02ab66db004c32fa46573bb1e/200624_A00834_0183_BHMTFYDRXX.tar.gz
\ No newline at end of file