Build branch craftbox/v0.3 with version v0.3.2 to craftbox on branch v0.3 (7d520dc)

Build pipeline: viash-hub.craftbox.v0.3.2-tpktm Source commit: 7d520dc76c Source message: Bump version to v0.3.2
Build branch craftbox/v0.3 with version v0.3.1 to craftbox on branch v0.3 (4acf73e)
2026-03-03 15:18:58 +00:00 · 2025-11-20 15:23:55 +00:00
43 changed files with 1072 additions and 735 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,21 @@
+# craftbox 0.3.2
+
+## NEW FEATURES
+
+* `move_files_to_directory`: add support for moving directories (PR #17).
+
+## MINOR CHANGES
+
+* Bump viash to 0.9.7 (PR #18).
+
+# craftbox 0.3.1
+
+## MINOR CHANGES
+
+* `concat_text`: Allow input files to be a mixed bag of gzipped and plain text files (PR #12).
+
+* `concat_text`: Stream concatenated files to gzip (PR #12).
+
 # craftbox 0.3.0

 ## NEW FEATURES
--- a/README.md
+++ b/README.md
@@ -43,7 +43,7 @@ Viash components in craftbox can be run in various ways:

 ``` mermaid lang="mermaid
 flowchart TD
-    A[craftbox v0.3.0] --> B(Viash Hub Launch)
+    A[craftbox v0.3.2] --> B(Viash Hub Launch)
    A --> C(Viash CLI)
    A --> D(Nextflow CLI)
    A --> E(Seqera Cloud)
@@ -53,7 +53,7 @@ flowchart TD
 ### 1. Via the Viash Hub Launch interface

 You can run this component directly from the Viash Hub [Launch
-interface](https://www.viash-hub.com/launch?package=craftbox&version=v0.3.0&component=concat_rtext&runner=Executable).
+interface](https://www.viash-hub.com/launch?package=craftbox&version=v0.3.2&component=concat_rtext&runner=Executable).

 ![](docs/viash-hub.png)

@@ -63,9 +63,9 @@ You can run this component directly from the command line using the
 Viash CLI.

 ``` bash
-viash run vsh://craftbox@v0.3.0/concat_rtext -- --help
+viash run vsh://craftbox@v0.3.2/concat_rtext -- --help

-viash run vsh://craftbox@v0.3.0/concat_rtext -- \
+viash run vsh://craftbox@v0.3.2/concat_rtext -- \
  --input path/to/input.txt \
  --input path/to/compressed.txt.gz \
  --output path/to/output.txt
@@ -80,7 +80,7 @@ You can run this component as a Nextflow pipeline.

 ``` bash
 nextflow run https://packages.viash-hub.com/vsh/craftbox \
-  -revision v0.3.0 \
+  -revision v0.3.2 \
  -main-script target/nextflow/concat_rtext/main.nf \
  -latest -resume \
  -profile docker \
@@ -109,7 +109,7 @@ component as a dependency:
 ``` yaml
 dependencies:
  - name: concat_rtext
-    repository: vsh://craftbox@v0.3.0
+    repository: vsh://craftbox@v0.3.2
 ```

 **Tip:** See the [Viash
--- a/README.qmd
+++ b/README.qmd
@@ -7,7 +7,7 @@ license <- paste0(package$links$repository, "/blob/main/LICENSE")
 contributing <- paste0(package$links$repository, "/blob/main/CONTRIBUTING.md")

 pkg <- package$name
-ver <- if (!is.null(package$version)) package$version else "v0.3.0"
+ver <- if (!is.null(package$version)) package$version else "v0.3.2"
 comp <- "concat_rtext"
 ```
 # 🪡📦 `r pkg`
--- a/_viash.yaml
+++ b/_viash.yaml
@@ -1,5 +1,5 @@
 name: craftbox
-version: v0.3.0
+version: v0.3.2
 summary: |
  A collection of custom-tailored scripts and applied utilities built with Viash.
 description: |
@@ -19,8 +19,7 @@ license: MIT
 links:
  issue_tracker: https://github.com/viash-hub/craftbox/issues
  repository: https://github.com/viash-hub/craftbox
-
-viash_version: 0.9.4
-
+viash_version: 0.9.7
 config_mods: |
  .requirements.commands := ['ps']
+organization: vsh
--- a/nextflow.config
+++ b/nextflow.config
@@ -1,6 +1,6 @@
 manifest {
  name = "craftbox"
-  version = "v0.3.0"
+  version = "v0.3.2"
  defaultBranch = "main"
  nextflowVersion = "!>=20.12.1-edge"
 }
--- a/src/concat_text/config.vsh.yaml
+++ b/src/concat_text/config.vsh.yaml
@@ -1,5 +1,5 @@
 name: concat_text
-summary: Concatenate a number of text files
+summary: Concatenate multiple (possibly gzipped) text files
 description: |
  Concatenate a number of text files, handle gzipped text files gracefully and
  optionally gzip the output text file.
@@ -11,12 +11,13 @@ authors:
    roles: [ author, maintainer ]
  - __merge__: /src/_authors/dries_schaumont.yaml
    roles: [ reviewer ]
+  - __merge__: /src/_authors/robrecht_cannoodt.yaml
+    roles: [ contributor ]

 info:
  improvements: |
-    This component could be improved in 2 ways:
-      1. Allow for a mix of zipped and plain input files
-      2. Allow to specify a compression algorithm for the output
+    This component could be improved:
+      1. Allow to specify a compression algorithm for the output

 argument_groups:
  - name: Input arguments
@@ -26,14 +27,14 @@ argument_groups:
        type: file
        multiple: true
        required: true
-        example: input?.txt.gz
+        example: input.txt.gz
  - name: Output arguments
    arguments:
      - name: "--gzip_output"
        type: boolean_true
        description: Should the output be zipped?
      - name: --output
-        description: File to write the output to, optionally gzipped.
+        description: File to write the output to, potentially gzipped.
        type: file
        direction: output
        example: output.txt
--- a/src/concat_text/script.sh
+++ b/src/concat_text/script.sh
@@ -1,34 +1,65 @@
 #!/usr/bin/env bash

-set -euo pipefail
+set -eo pipefail

-TMPDIR=$(mktemp -d "$meta_temp_dir/concat_text-XXXXXX")
-function clean_up {
-  [[ -d "$TMPDIR" ]] && rm -r "$TMPDIR"
+## VIASH START
+par_input="README.md;README.qmd"
+par_output="concatenated_output.txt"
+par_compress_output="true"
+## VIASH END
+
+# --- Function to check for GZIP format using the 'file' command ---
+is_gzipped() {
+    # Ensure the file exists and is not empty before checking
+    if [ ! -s "$1" ]; then
+        return 1
+    fi
+    # Get the MIME type of the file. The '-b' option omits the filename from the output.
+    local mime_type
+    mime_type=$(file -b --mime-type "$1")
+    
+    # Check if the MIME type corresponds to gzip.
+    # application/gzip is standard, while application/x-gzip is also commonly seen.
+    if [[ "$mime_type" == "application/gzip" || "$mime_type" == "application/x-gzip" ]]; then
+        return 0 # 0 indicates success (true in bash)
+    else
+        return 1 # 1 indicates failure (false in bash)
+    fi
 }
-trap clean_up EXIT

-par_input="$(echo "$par_input" | tr ';' ' ')"
+# Read the ;-separated file paths from the input variable into an array
+IFS=";" read -ra input_files <<< "$par_input"

-echo -n ">> Check if input is gzipped... "
-set +eo pipefail
-file $par_input | grep -q 'gzip'
-is_zipped="$?"
-set -euo pipefail
-[[ "$is_zipped" == "0" ]] && echo "yes" || echo "no"
+# Process the files if the array contains any paths
+if [ ${#input_files[@]} -gt 0 ] && [ -n "${input_files[0]}" ]; then

-if [[ "$is_zipped" == "0" ]]; then
-  echo ">> zcat gzipped files"
-  zcat $par_input > $TMPDIR/contents
+    # Ensure the output file is empty before we start
+    > "$par_output"
+
+    echo "Processing files for -> $par_output"
+
+    # Create a subshell for the loop to group all cat/zcat output.
+    (
+        for file in "${input_files[@]}"; do
+            if [ -z "$file" ]; then continue; fi # Skip empty entries in the array
+
+            if is_gzipped "$file"; then
+                zcat "$file"
+            else
+                cat "$file"
+            fi
+        done
+    ) | if [ "$par_compress_output" = "true" ]; then
+        # If compression is enabled, pipe the entire stream to gzip
+        gzip -c >> "$par_output"
+    else
+        # Otherwise, just redirect the stream to the plain text file
+        cat >> "$par_output"
+    fi
+
+    echo "Finished creating $par_output."
 else
-  echo ">> cat plain files"
-  cat $par_input > $TMPDIR/contents
+    echo "No input files provided in \$par_input. Exiting."
 fi

-if [ "$par_gzip_output" == true ]; then
-  echo ">> Zip output file"
-  gzip $TMPDIR/contents
-  mv $TMPDIR/contents.gz $par_output
-else
-  mv $TMPDIR/contents $par_output
-fi
+echo "Script finished successfully."
--- a/src/concat_text/test.sh
+++ b/src/concat_text/test.sh
@@ -2,6 +2,65 @@

 set -euo pipefail

+echo ">> Running concat_text.sh script"
+
+is_gzipped() {
+    # Ensure the file exists and is not empty
+    if [ ! -s "$1" ]; then
+        return 1
+    fi
+    # Get the MIME type of the file
+    local mime_type
+    mime_type=$(file -b --mime-type "$1")
+    
+    # Check if the MIME type corresponds to gzip.
+    if [[ "$mime_type" == "application/gzip" || "$mime_type" == "application/x-gzip" ]]; then
+        return 0
+    else
+        return 1
+    fi
+}
+
+compare_files() {
+  local file1="$1"
+  local file2="$2"
+  if [[ ! -f "$file1" || ! -f "$file2" ]]; then
+    echo "One of the files does not exist: $file1 or $file2"
+    return 1
+  fi
+  # decompress file 1 if need be
+  if is_gzipped "$file1"; then
+    file1=$(mktemp)
+    zcat "$1" > "$file1"
+  fi
+  # decompress file 2 if need be
+  if is_gzipped "$file2"; then
+    file2=$(mktemp)
+    zcat "$2" > "$file2"
+  fi
+
+  if cmp -s "$file1" "$file2"; then
+    echo "Files are identical."
+    return 0
+  else
+    echo "Files differ."
+    echo "Found:"
+    if is_gzipped "$file1"; then
+      zcat "$file1" | od -c
+    else
+      cat "$file1" | od -c
+    fi
+    echo "Expected:"
+    if is_gzipped "$file2"; then
+      zcat "$file2" | od -c
+    else
+      cat "$file2" | od -c
+    fi
+    return 1
+  fi
+}
+
+## TEST RESOURCES
 echo ">> Creating test input files file[1-3].txt"
 INPUT_FILE_1="file1.txt"
 INPUT_FILE_2="file2.txt"
@@ -25,46 +84,31 @@ EOF

 gzip -k "expected_output.txt"

+## RUN TESTS
 echo ">> Run component on 3 plain input files, plain output"
 $meta_executable \
  --input "$INPUT_FILE_1;$INPUT_FILE_2;$INPUT_FILE_3" \
  --output "output1.txt"
+compare_files "output1.txt" "expected_output.txt"

-[[ ! -f "output1.txt" ]] \
-  && echo "Output file output1.txt not found!" && exit 1
-[[ $(cmp "output1.txt" "expected_output.txt") ]] \
-  && echo "Output file output1.txt is not as expected!" && exit 1
-
-echo ">> Run component on 3 zipped input files, plain output"
+echo ">> Run component on mixed input files, plain output"
 $meta_executable \
-  --input "$INPUT_FILE_1.gz;$INPUT_FILE_2.gz;$INPUT_FILE_3.gz" \
+  --input "$INPUT_FILE_1.gz;$INPUT_FILE_2;$INPUT_FILE_3.gz" \
  --output "output2.txt"
-
-[[ ! -f "output2.txt" ]] \
-  && echo "Output file output2.txt not found!" && exit 1
-[[ $(cmp "output2.txt" "expected_output.txt") ]] \
-  && echo "Output file output2.txt is not as expected!" && exit 1
+compare_files "output2.txt" "expected_output.txt"

 echo ">> Run component on 3 plain input files, zipped output"
 $meta_executable \
  --input "$INPUT_FILE_1;$INPUT_FILE_2;$INPUT_FILE_3" \
  --output "output3.txt.gz" \
  --gzip_output
+compare_files "output3.txt.gz" "expected_output.txt.gz"

-[[ ! -f "output3.txt.gz" ]] \
-  && echo "Output file output3.txt.gz not found!" && exit 1
-[[ $(cmp "output3.txt.gz" "expected_output.txt.gz") ]] \
-  && echo "Output file output3.txt.gz is not as expected!" && exit 1
-
-echo ">> Run component on 3 zipped input files, zipped output"
+echo ">> Run component on mixed input files, zipped output"
 $meta_executable \
-  --input "$INPUT_FILE_1.gz;$INPUT_FILE_2.gz;$INPUT_FILE_3.gz" \
+  --input "$INPUT_FILE_1.gz;$INPUT_FILE_2;$INPUT_FILE_3.gz" \
  --output "output4.txt.gz" \
  --gzip_output
-
-[[ ! -f "output4.txt.gz" ]] \
-  && echo "Output file output4.txt.gz not found!" && exit 1
-[[ $(cmp "output4.txt.gz" "expected_output.txt.gz") ]] \
-  && echo "Output file output4.txt.gz is not as expected!" && exit 1
+compare_files "output4.txt.gz" "expected_output.txt.gz"

 echo ">> Tests done"
--- a/src/move_files_to_directory/config.vsh.yaml
+++ b/src/move_files_to_directory/config.vsh.yaml
@@ -1,39 +1,52 @@
 name: move_files_to_directory
-summary: Publish one or multiple files to the same directory
-description: This component copies one or multiple files to the same destination directory, creating the output directory if it doesn't exist.
+summary: Publish one or multiple files or directories to the same output directory.
+description: |
+  This component copies one or multiple files or directories
+  to the same destination directory, creating the output directory if it doesn't
+  exist.
 authors:
  - __merge__: /src/_authors/dorien_roosen.yaml
    roles: [ maintainer ]
-arguments:
-  - name: "--input"
-    type: file
-    direction: input
-    required: true
-    multiple: true
-    description: Paths of the files that will be copied into the output directory.
-  - name: "--output"
-    type: file
-    direction: output
-    required: true
-    description: Path to output directory
-  - name: "--keep_symbolic_links"
-    alternatives: [-d]
-    type: boolean_true
-    description: Preserve symbolic links.
+
+argument_groups:
+  - name: Inputs
+    arguments:
+      - name: "--input"
+        type: file
+        direction: input
+        required: true
+        multiple: true
+        description: Paths of the files or directories that will be copied into the output directory.
+  - name: Outputs
+    arguments:
+      - name: "--output"
+        type: file
+        direction: output
+        required: true
+        description: Path to output directory.
+  - name: Options
+    arguments:
+      - name: "--keep_symbolic_links"
+        type: boolean_true
+        description: When set, symbolic links are preserved as symbolic links in the output directory. By default, symbolic links are dereferenced and the target file is copied.
+
 resources:
  - type: bash_script
    path: script.sh
+
 test_resources:
  - type: bash_script
    path: test.sh

 engines:
- type: docker
-  image: debian:latest
-  setup:
+  - type: docker
+    image: debian:latest
+    setup:
      - type: apt
-        packages: [procps]
+        packages:
+          - procps
+  - type: native

 runners:
- type: executable
- type: nextflow
+  - type: executable
+  - type: nextflow
--- a/src/move_files_to_directory/script.sh
+++ b/src/move_files_to_directory/script.sh
@@ -3,30 +3,37 @@
 set -eo pipefail

 ## VIASH START
-par_input="input.txt;input_2.txt"
+par_input="input.txt;input_dir.zarr"
 par_output="output"
+par_keep_symbolic_links="false"
 ## VIASH END

-
 if [[ ! -d "$par_output" ]]; then
  mkdir -p "$par_output"
 fi

-extra_params=( )
-
-if [ "$par_keep_symbolic_links" == "true" ]; then
-  extra_params+=( "-d" )
+# Set copy flags based on options
+if [[ "$par_keep_symbolic_links" == "true" ]]; then
+  # -a implies -dR --preserve=all
+  # with -d: same as --no-dereference (and --preserve=links)
+  # and --no-dereference: never follow symbolic links in SOURCE
+  # and -R, -r, --recursive: copy directories recursively
+  # --keep-directory-symlink: if the destination already exists and is a
+  #   symbolic link to a directory, follow the symlink and copy into the directory
+  #   it points to, instead of removing the symlink and creating a real directory in its place.
+  cp_flags="-a --keep-directory-symlink"
+else
+  # -L: always follow symbolic links in SOURCE
+  cp_flags="-Lr --preserve=all --no-preserve=link --keep-directory-symlink"
 fi

-# Process multiple input files
-IFS=";" read -ra input_files <<< "$par_input"
-for file in "${input_files[@]}"; do
-  # Check if the file exists before copying
-  if [[ -f "$file" ]]; then
-
-    cp ${extra_params[@]} "$file" "$par_output/"
-    echo "Copied $file to $par_output/"
+# Process multiple input paths (files or directories)
+IFS=";" read -ra input_paths <<< "$par_input"
+for path in "${input_paths[@]}"; do
+  if [[ -e "$path" ]] || [[ -L "$path" ]]; then
+    cp $cp_flags "$path" "$par_output/"
+    echo "Copied $path to $par_output/"
  else
-    echo "Warning: Input file $file does not exist, skipping"
+    echo "Warning: Input path $path does not exist, skipping"
  fi
 done
--- a/src/move_files_to_directory/test.sh
+++ b/src/move_files_to_directory/test.sh
@@ -11,7 +11,7 @@ trap clean_up EXIT
 touch "$TMPDIR/test_file.txt"
 touch "$TMPDIR/another_file.txt"

-./move_files_to_directory \
+$meta_executable \
  --input "$TMPDIR/test_file.txt" \
  --input "$TMPDIR/another_file.txt" \
  --output "$TMPDIR/test_output"
@@ -19,9 +19,23 @@ touch "$TMPDIR/another_file.txt"
 [[ ! -d "$TMPDIR/test_output" ]] && echo "It seems no output directory is generated" && exit 1
 [[ ! -f "$TMPDIR/test_output/test_file.txt" ]] && [[ ! -f test_output/another_file.txt ]] && echo "Output files were not copied to the output directory" && exit 1

+# Test copying a directory
+mkdir -p "$TMPDIR/test_dir"
+touch "$TMPDIR/test_dir/file_in_dir.txt"
+touch "$TMPDIR/test_dir/another_file_in_dir.txt"
+
+$meta_executable \
+  --input "$TMPDIR/test_dir" \
+  --output "$TMPDIR/test_output_dir"
+
+[[ ! -d "$TMPDIR/test_output_dir" ]] && echo "It seems no output directory (test_output_dir) is generated" && exit 1
+[[ ! -d "$TMPDIR/test_output_dir/test_dir" ]] && echo "Input directory was not copied to the output directory" && exit 1
+[[ ! -f "$TMPDIR/test_output_dir/test_dir/file_in_dir.txt" ]] && echo "Files inside the copied directory are missing" && exit 1
+[[ ! -f "$TMPDIR/test_output_dir/test_dir/another_file_in_dir.txt" ]] && echo "Files inside the copied directory are missing" && exit 1
+
 ln -s "$TMPDIR/test_file.txt" "$TMPDIR/symlink.txt"

-./move_files_to_directory \
+$meta_executable \
  --input "$TMPDIR/symlink.txt" \
  --output "$TMPDIR/test_output_symlink" \
  --keep_symbolic_links
--- a/target/executable/check_disk_space/.config.vsh.yaml
+++ b/target/executable/check_disk_space/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "check_disk_space"
-version: "v0.3.0"
+version: "v0.3.2"
 argument_groups:
 - name: "Inputs"
  arguments:
@@ -144,7 +144,7 @@ engines:
  id: "docker"
  image: "bash:latest"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.0"
+  target_tag: "v0.3.2"
  namespace_separator: "/"
  entrypoint: []
  cmd: null
@@ -156,13 +156,12 @@ build_info:
  engine: "docker|native"
  output: "target/executable/check_disk_space"
  executable: "target/executable/check_disk_space/check_disk_space"
-  viash_version: "0.9.4"
-  git_commit: "a1801c5139bbcda244e06affa66d16f7abd5e124"
+  viash_version: "0.9.7"
+  git_commit: "7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9"
  git_remote: "https://github.com/viash-hub/craftbox"
-  git_tag: "v0.1.0-11-ga1801c5"
 package_config:
  name: "craftbox"
-  version: "v0.3.0"
+  version: "v0.3.2"
  summary: "A collection of custom-tailored scripts and applied utilities built with\
    \ Viash.\n"
  description: "`craftbox` is a curated collection of custom scripts and utilities\
@@ -178,14 +177,14 @@ package_config:
    \ to ensure dependency management and a consistent, reproducible runtime environment.\n\
    \    * Unit tested where applicable to ensure components function as expected.\n"
  info: null
-  viash_version: "0.9.4"
+  viash_version: "0.9.7"
  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 := 'v0.3.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
  keywords:
  - "scripts"
  - "custom"
--- a/target/executable/check_disk_space/check_disk_space
+++ b/target/executable/check_disk_space/check_disk_space
@@ -1,8 +1,8 @@
 #!/usr/bin/env bash

-# check_disk_space v0.3.0
+# check_disk_space v0.3.2
 # 
-# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.7 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -446,10 +446,10 @@ function ViashDockerfile {
 FROM bash:latest
 ENTRYPOINT []
 LABEL org.opencontainers.image.description="Companion container for running component check_disk_space"
-LABEL org.opencontainers.image.created="2025-08-28T13:48:17Z"
+LABEL org.opencontainers.image.created="2026-03-03T15:11:57Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/craftbox"
-LABEL org.opencontainers.image.revision="a1801c5139bbcda244e06affa66d16f7abd5e124"
-LABEL org.opencontainers.image.version="v0.3.0"
+LABEL org.opencontainers.image.revision="7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9"
+LABEL org.opencontainers.image.version="v0.3.2"

 VIASHDOCKER
  fi
@@ -566,7 +566,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "check_disk_space v0.3.0"
+  echo "check_disk_space v0.3.2"
  echo ""
  echo "Check for available disk space on the system."
  echo ""
@@ -648,7 +648,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "check_disk_space v0.3.0"
+            echo "check_disk_space v0.3.2"
            exit
            ;;
        --tmp_space_required)
@@ -783,7 +783,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/craftbox/check_disk_space:v0.3.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/craftbox/check_disk_space:v0.3.2'
  fi

  # print dockerfile
--- a/target/executable/concat_text/.config.vsh.yaml
+++ b/target/executable/concat_text/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "concat_text"
-version: "v0.3.0"
+version: "v0.3.2"
 authors:
 - name: "Toni Verbeiren"
  roles:
@@ -26,6 +26,22 @@ authors:
    - name: "Data Intuitive"
      href: "https://www.data-intuitive.com"
      role: "Data Scientist"
+- name: "Robrecht Cannoodt"
+  roles:
+  - "contributor"
+  info:
+    links:
+      email: "robrecht@data-intuitive.com"
+      github: "rcannood"
+      orcid: "0000-0003-3641-729X"
+      linkedin: "robrechtcannoodt"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Science Engineer"
+    - name: "Open Problems"
+      href: "https://openproblems.bio"
+      role: "Core Member"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -34,7 +50,7 @@ argument_groups:
    description: "A list of (gzipped) text files."
    info: null
    example:
-    - "input?.txt.gz"
+    - "input.txt.gz"
    must_exist: true
    create_parent: true
    required: true
@@ -50,7 +66,7 @@ argument_groups:
    direction: "input"
  - type: "file"
    name: "--output"
-    description: "File to write the output to, optionally gzipped."
+    description: "File to write the output to, potentially gzipped."
    info: null
    example:
    - "output.txt"
@@ -64,7 +80,7 @@ resources:
 - type: "bash_script"
  path: "script.sh"
  is_executable: true
-summary: "Concatenate a number of text files"
+summary: "Concatenate multiple (possibly gzipped) text files"
 description: "Concatenate a number of text files, handle gzipped text files gracefully\
  \ and\noptionally gzip the output text file.\n\nThis component is useful for concatening\
  \ fastq files from different lanes, for instance.\n"
@@ -73,9 +89,8 @@ test_resources:
  path: "test.sh"
  is_executable: true
 info:
-  improvements: "This component could be improved in 2 ways:\n  1. Allow for a mix\
-    \ of zipped and plain input files\n  2. Allow to specify a compression algorithm\
-    \ for the output\n"
+  improvements: "This component could be improved:\n  1. Allow to specify a compression\
+    \ algorithm for the output\n"
 status: "enabled"
 scope:
  image: "public"
@@ -156,7 +171,7 @@ engines:
  id: "docker"
  image: "alpine:latest"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.0"
+  target_tag: "v0.3.2"
  namespace_separator: "/"
  setup:
  - type: "apk"
@@ -174,13 +189,12 @@ build_info:
  engine: "docker|native"
  output: "target/executable/concat_text"
  executable: "target/executable/concat_text/concat_text"
-  viash_version: "0.9.4"
-  git_commit: "a1801c5139bbcda244e06affa66d16f7abd5e124"
+  viash_version: "0.9.7"
+  git_commit: "7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9"
  git_remote: "https://github.com/viash-hub/craftbox"
-  git_tag: "v0.1.0-11-ga1801c5"
 package_config:
  name: "craftbox"
-  version: "v0.3.0"
+  version: "v0.3.2"
  summary: "A collection of custom-tailored scripts and applied utilities built with\
    \ Viash.\n"
  description: "`craftbox` is a curated collection of custom scripts and utilities\
@@ -196,14 +210,14 @@ package_config:
    \ to ensure dependency management and a consistent, reproducible runtime environment.\n\
    \    * Unit tested where applicable to ensure components function as expected.\n"
  info: null
-  viash_version: "0.9.4"
+  viash_version: "0.9.7"
  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 := 'v0.3.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
  keywords:
  - "scripts"
  - "custom"
--- a/target/executable/concat_text/concat_text
+++ b/target/executable/concat_text/concat_text
@@ -1,8 +1,8 @@
 #!/usr/bin/env bash

-# concat_text v0.3.0
+# concat_text v0.3.2
 # 
-# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.7 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -14,6 +14,7 @@
 # Component authors:
 #  * Toni Verbeiren (author, maintainer)
 #  * Dries Schaumont (reviewer)
+#  * Robrecht Cannoodt (contributor)

 set -e

@@ -451,12 +452,12 @@ FROM alpine:latest
 ENTRYPOINT []
 RUN apk add --no-cache bash procps file

-LABEL org.opencontainers.image.authors="Toni Verbeiren, Dries Schaumont"
+LABEL org.opencontainers.image.authors="Toni Verbeiren, Dries Schaumont, Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component concat_text"
-LABEL org.opencontainers.image.created="2025-08-28T13:48:17Z"
+LABEL org.opencontainers.image.created="2026-03-03T15:11:58Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/craftbox"
-LABEL org.opencontainers.image.revision="a1801c5139bbcda244e06affa66d16f7abd5e124"
-LABEL org.opencontainers.image.version="v0.3.0"
+LABEL org.opencontainers.image.revision="7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9"
+LABEL org.opencontainers.image.version="v0.3.2"

 VIASHDOCKER
  fi
@@ -573,7 +574,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "concat_text v0.3.0"
+  echo "concat_text v0.3.2"
  echo ""
  echo "Concatenate a number of text files, handle gzipped text files gracefully and"
  echo "optionally gzip the output text file."
@@ -584,7 +585,7 @@ function ViashHelp {
  echo "Input arguments:"
  echo "    --input"
  echo "        type: file, required parameter, multiple values allowed, file must exist"
-  echo "        example: input?.txt.gz"
+  echo "        example: input.txt.gz"
  echo "        A list of (gzipped) text files."
  echo ""
  echo "Output arguments:"
@@ -595,7 +596,7 @@ function ViashHelp {
  echo "    --output"
  echo "        type: file, output, file must exist"
  echo "        example: output.txt"
-  echo "        File to write the output to, optionally gzipped."
+  echo "        File to write the output to, potentially gzipped."
  echo ""
  echo "Viash built in Computational Requirements:"
  echo "    ---cpus=INT"
@@ -644,7 +645,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "concat_text v0.3.0"
+            echo "concat_text v0.3.2"
            exit
            ;;
        --input)
@@ -768,7 +769,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/craftbox/concat_text:v0.3.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/craftbox/concat_text:v0.3.2'
  fi

  # print dockerfile
@@ -1080,6 +1081,10 @@ function interrupt {
 trap clean_up EXIT
 trap interrupt INT SIGINT
 cat > "\$tempscript" << 'VIASHMAIN'
+#!/usr/bin/env bash
+
+set -eo pipefail
+
 ## VIASH START
 # The following code has been auto-generated by Viash.
 $( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "${VIASH_PAR_INPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_input='&'#" ; else echo "# par_input="; fi )
@@ -1105,40 +1110,62 @@ $( if [ ! -z ${VIASH_META_MEMORY_TIB+x} ]; then echo "${VIASH_META_MEMORY_TIB}"
 $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_pib='&'#" ; else echo "# meta_memory_pib="; fi )

 ## VIASH END
-#!/usr/bin/env bash

-set -euo pipefail
-
-TMPDIR=\$(mktemp -d "\$meta_temp_dir/concat_text-XXXXXX")
-function clean_up {
-  [[ -d "\$TMPDIR" ]] && rm -r "\$TMPDIR"
+# --- Function to check for GZIP format using the 'file' command ---
+is_gzipped() {
+    # Ensure the file exists and is not empty before checking
+    if [ ! -s "\$1" ]; then
+        return 1
+    fi
+    # Get the MIME type of the file. The '-b' option omits the filename from the output.
+    local mime_type
+    mime_type=\$(file -b --mime-type "\$1")
+    
+    # Check if the MIME type corresponds to gzip.
+    # application/gzip is standard, while application/x-gzip is also commonly seen.
+    if [[ "\$mime_type" == "application/gzip" || "\$mime_type" == "application/x-gzip" ]]; then
+        return 0 # 0 indicates success (true in bash)
+    else
+        return 1 # 1 indicates failure (false in bash)
+    fi
 }
-trap clean_up EXIT

-par_input="\$(echo "\$par_input" | tr ';' ' ')"
+# Read the ;-separated file paths from the input variable into an array
+IFS=";" read -ra input_files <<< "\$par_input"

-echo -n ">> Check if input is gzipped... "
-set +eo pipefail
-file \$par_input | grep -q 'gzip'
-is_zipped="\$?"
-set -euo pipefail
-[[ "\$is_zipped" == "0" ]] && echo "yes" || echo "no"
+# Process the files if the array contains any paths
+if [ \${#input_files[@]} -gt 0 ] && [ -n "\${input_files[0]}" ]; then

-if [[ "\$is_zipped" == "0" ]]; then
-  echo ">> zcat gzipped files"
-  zcat \$par_input > \$TMPDIR/contents
+    # Ensure the output file is empty before we start
+    > "\$par_output"
+
+    echo "Processing files for -> \$par_output"
+
+    # Create a subshell for the loop to group all cat/zcat output.
+    (
+        for file in "\${input_files[@]}"; do
+            if [ -z "\$file" ]; then continue; fi # Skip empty entries in the array
+
+            if is_gzipped "\$file"; then
+                zcat "\$file"
+            else
+                cat "\$file"
+            fi
+        done
+    ) | if [ "\$par_compress_output" = "true" ]; then
+        # If compression is enabled, pipe the entire stream to gzip
+        gzip -c >> "\$par_output"
+    else
+        # Otherwise, just redirect the stream to the plain text file
+        cat >> "\$par_output"
+    fi
+
+    echo "Finished creating \$par_output."
 else
-  echo ">> cat plain files"
-  cat \$par_input > \$TMPDIR/contents
+    echo "No input files provided in \\\$par_input. Exiting."
 fi

-if [ "\$par_gzip_output" == true ]; then
-  echo ">> Zip output file"
-  gzip \$TMPDIR/contents
-  mv \$TMPDIR/contents.gz \$par_output
-else
-  mv \$TMPDIR/contents \$par_output
-fi
+echo "Script finished successfully."
 VIASHMAIN
 bash "\$tempscript" &
 wait "\$!"
--- a/target/executable/csv2fasta/.config.vsh.yaml
+++ b/target/executable/csv2fasta/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "csv2fasta"
-version: "v0.3.0"
+version: "v0.3.2"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -227,7 +227,7 @@ engines:
  id: "docker"
  image: "python:slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.0"
+  target_tag: "v0.3.2"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -256,13 +256,12 @@ build_info:
  engine: "docker|native"
  output: "target/executable/csv2fasta"
  executable: "target/executable/csv2fasta/csv2fasta"
-  viash_version: "0.9.4"
-  git_commit: "a1801c5139bbcda244e06affa66d16f7abd5e124"
+  viash_version: "0.9.7"
+  git_commit: "7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9"
  git_remote: "https://github.com/viash-hub/craftbox"
-  git_tag: "v0.1.0-11-ga1801c5"
 package_config:
  name: "craftbox"
-  version: "v0.3.0"
+  version: "v0.3.2"
  summary: "A collection of custom-tailored scripts and applied utilities built with\
    \ Viash.\n"
  description: "`craftbox` is a curated collection of custom scripts and utilities\
@@ -278,14 +277,14 @@ package_config:
    \ to ensure dependency management and a consistent, reproducible runtime environment.\n\
    \    * Unit tested where applicable to ensure components function as expected.\n"
  info: null
-  viash_version: "0.9.4"
+  viash_version: "0.9.7"
  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 := 'v0.3.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
  keywords:
  - "scripts"
  - "custom"
--- a/target/executable/csv2fasta/csv2fasta
+++ b/target/executable/csv2fasta/csv2fasta
@@ -1,8 +1,8 @@
 #!/usr/bin/env bash

-# csv2fasta v0.3.0
+# csv2fasta v0.3.2
 # 
-# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.7 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \

 LABEL org.opencontainers.image.authors="Dries Schaumont, Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component csv2fasta"
-LABEL org.opencontainers.image.created="2025-08-28T13:48:17Z"
+LABEL org.opencontainers.image.created="2026-03-03T15:11:58Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/craftbox"
-LABEL org.opencontainers.image.revision="a1801c5139bbcda244e06affa66d16f7abd5e124"
-LABEL org.opencontainers.image.version="v0.3.0"
+LABEL org.opencontainers.image.revision="7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9"
+LABEL org.opencontainers.image.version="v0.3.2"

 VIASHDOCKER
  fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "csv2fasta v0.3.0"
+  echo "csv2fasta v0.3.2"
  echo ""
  echo "Convert two columns from a CSV file to FASTA entries. The CSV file can"
  echo "contain an optional header and each row (other than the header) becomes"
@@ -695,7 +695,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "csv2fasta v0.3.0"
+            echo "csv2fasta v0.3.2"
            exit
            ;;
        --input)
@@ -879,7 +879,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/craftbox/csv2fasta:v0.3.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/craftbox/csv2fasta:v0.3.2'
  fi

  # print dockerfile
--- a/target/executable/move_files_to_directory/.config.vsh.yaml
+++ b/target/executable/move_files_to_directory/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "move_files_to_directory"
-version: "v0.3.0"
+version: "v0.3.2"
 authors:
 - name: "Dorien Roosen"
  roles:
@@ -14,11 +14,12 @@ authors:
      href: "https://www.data-intuitive.com"
      role: "Data Scientist"
 argument_groups:
- name: "Arguments"
+- name: "Inputs"
  arguments:
  - type: "file"
    name: "--input"
-    description: "Paths of the files that will be copied into the output directory."
+    description: "Paths of the files or directories that will be copied into the output\
+      \ directory."
    info: null
    must_exist: true
    create_parent: true
@@ -26,9 +27,11 @@ argument_groups:
    direction: "input"
    multiple: true
    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
  - type: "file"
    name: "--output"
-    description: "Path to output directory"
+    description: "Path to output directory."
    info: null
    must_exist: true
    create_parent: true
@@ -36,20 +39,22 @@ argument_groups:
    direction: "output"
    multiple: false
    multiple_sep: ";"
+- name: "Options"
+  arguments:
  - type: "boolean_true"
    name: "--keep_symbolic_links"
-    alternatives:
-    - "-d"
-    description: "Preserve symbolic links."
+    description: "When set, symbolic links are preserved as symbolic links in the\
+      \ output directory. By default, symbolic links are dereferenced and the target\
+      \ file is copied."
    info: null
    direction: "input"
 resources:
 - type: "bash_script"
  path: "script.sh"
  is_executable: true
-summary: "Publish one or multiple files to the same directory"
-description: "This component copies one or multiple files to the same destination\
-  \ directory, creating the output directory if it doesn't exist."
+summary: "Publish one or multiple files or directories to the same output directory."
+description: "This component copies one or multiple files or directories\nto the same\
+  \ destination directory, creating the output directory if it doesn't\nexist.\n"
 test_resources:
 - type: "bash_script"
  path: "test.sh"
@@ -135,7 +140,7 @@ engines:
  id: "docker"
  image: "debian:latest"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.0"
+  target_tag: "v0.3.2"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -146,19 +151,20 @@ engines:
  cmd: null
 - type: "native"
  id: "native"
+- type: "native"
+  id: "native"
 build_info:
  config: "src/move_files_to_directory/config.vsh.yaml"
  runner: "executable"
-  engine: "docker|native"
+  engine: "docker|native|native"
  output: "target/executable/move_files_to_directory"
  executable: "target/executable/move_files_to_directory/move_files_to_directory"
-  viash_version: "0.9.4"
-  git_commit: "a1801c5139bbcda244e06affa66d16f7abd5e124"
+  viash_version: "0.9.7"
+  git_commit: "7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9"
  git_remote: "https://github.com/viash-hub/craftbox"
-  git_tag: "v0.1.0-11-ga1801c5"
 package_config:
  name: "craftbox"
-  version: "v0.3.0"
+  version: "v0.3.2"
  summary: "A collection of custom-tailored scripts and applied utilities built with\
    \ Viash.\n"
  description: "`craftbox` is a curated collection of custom scripts and utilities\
@@ -174,14 +180,14 @@ package_config:
    \ to ensure dependency management and a consistent, reproducible runtime environment.\n\
    \    * Unit tested where applicable to ensure components function as expected.\n"
  info: null
-  viash_version: "0.9.4"
+  viash_version: "0.9.7"
  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 := 'v0.3.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
  keywords:
  - "scripts"
  - "custom"
--- a/target/executable/move_files_to_directory/move_files_to_directory
+++ b/target/executable/move_files_to_directory/move_files_to_directory
@@ -1,8 +1,8 @@
 #!/usr/bin/env bash

-# move_files_to_directory v0.3.0
+# move_files_to_directory v0.3.2
 # 
-# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.7 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -454,10 +454,10 @@ RUN apt-get update && \

 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component move_files_to_directory"
-LABEL org.opencontainers.image.created="2025-08-28T13:48:17Z"
+LABEL org.opencontainers.image.created="2026-03-03T15:11:58Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/craftbox"
-LABEL org.opencontainers.image.revision="a1801c5139bbcda244e06affa66d16f7abd5e124"
-LABEL org.opencontainers.image.version="v0.3.0"
+LABEL org.opencontainers.image.revision="7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9"
+LABEL org.opencontainers.image.version="v0.3.2"

 VIASHDOCKER
  fi
@@ -574,23 +574,29 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "move_files_to_directory v0.3.0"
+  echo "move_files_to_directory v0.3.2"
  echo ""
-  echo "This component copies one or multiple files to the same destination directory,"
-  echo "creating the output directory if it doesn't exist."
+  echo "This component copies one or multiple files or directories"
+  echo "to the same destination directory, creating the output directory if it doesn't"
+  echo "exist."
  echo ""
-  echo "Arguments:"
+  echo "Inputs:"
  echo "    --input"
  echo "        type: file, required parameter, multiple values allowed, file must exist"
-  echo "        Paths of the files that will be copied into the output directory."
+  echo "        Paths of the files or directories that will be copied into the output"
+  echo "        directory."
  echo ""
+  echo "Outputs:"
  echo "    --output"
  echo "        type: file, required parameter, output, file must exist"
-  echo "        Path to output directory"
+  echo "        Path to output directory."
  echo ""
-  echo "    -d, --keep_symbolic_links"
+  echo "Options:"
+  echo "    --keep_symbolic_links"
  echo "        type: boolean_true"
-  echo "        Preserve symbolic links."
+  echo "        When set, symbolic links are preserved as symbolic links in the output"
+  echo "        directory. By default, symbolic links are dereferenced and the target"
+  echo "        file is copied."
  echo ""
  echo "Viash built in Computational Requirements:"
  echo "    ---cpus=INT"
@@ -613,7 +619,7 @@ function ViashHelp {
  echo ""
  echo "Viash built in Engines:"
  echo "    ---engine=ENGINE_ID"
-  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Specify the engine to use. Options are: docker, native, native."
  echo "        Default: docker"
 }

@@ -639,7 +645,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "move_files_to_directory v0.3.0"
+            echo "move_files_to_directory v0.3.2"
            exit
            ;;
        --input)
@@ -675,11 +681,6 @@ while [[ $# -gt 0 ]]; do
            VIASH_PAR_KEEP_SYMBOLIC_LINKS=true
            shift 1
            ;;
-        -d)
-            [ -n "$VIASH_PAR_KEEP_SYMBOLIC_LINKS" ] && ViashError Bad arguments for option \'-d\': \'$VIASH_PAR_KEEP_SYMBOLIC_LINKS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
-            VIASH_PAR_KEEP_SYMBOLIC_LINKS=true
-            shift 1
-            ;;
        ---engine)
            VIASH_ENGINE_ID="$2"
            shift 2
@@ -753,12 +754,12 @@ done
 eval set -- $VIASH_POSITIONAL_ARGS


-if   [ "$VIASH_ENGINE_ID" == "native" ]  ; then
+if   [ "$VIASH_ENGINE_ID" == "native" ]  ||  [ "$VIASH_ENGINE_ID" == "native" ]  ; then
  VIASH_ENGINE_TYPE='native'
 elif   [ "$VIASH_ENGINE_ID" == "docker" ]  ; then
  VIASH_ENGINE_TYPE='docker'
 else
-  ViashError "Engine '$VIASH_ENGINE_ID' is not recognized. Options are: docker, native."
+  ViashError "Engine '$VIASH_ENGINE_ID' is not recognized. Options are: docker, native, native."
  exit 1
 fi

@@ -768,7 +769,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/craftbox/move_files_to_directory:v0.3.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/craftbox/move_files_to_directory:v0.3.2'
  fi

  # print dockerfile
@@ -989,7 +990,7 @@ if [ ! -z "$VIASH_PAR_OUTPUT" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT")" ]; th
  mkdir -p "$(dirname "$VIASH_PAR_OUTPUT")"
 fi

-if  [ "$VIASH_ENGINE_ID" == "native" ]  ; then
+if  [ "$VIASH_ENGINE_ID" == "native" ]  ||  [ "$VIASH_ENGINE_ID" == "native" ]  ; then
  if [ "$VIASH_MODE" == "run" ]; then
    VIASH_CMD="bash"
  else
@@ -1114,27 +1115,33 @@ $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}"

 ## VIASH END

-
 if [[ ! -d "\$par_output" ]]; then
  mkdir -p "\$par_output"
 fi

-extra_params=( )
-
-if [ "\$par_keep_symbolic_links" == "true" ]; then
-  extra_params+=( "-d" )
+# Set copy flags based on options
+if [[ "\$par_keep_symbolic_links" == "true" ]]; then
+  # -a implies -dR --preserve=all
+  # with -d: same as --no-dereference (and --preserve=links)
+  # and --no-dereference: never follow symbolic links in SOURCE
+  # and -R, -r, --recursive: copy directories recursively
+  # --keep-directory-symlink: if the destination already exists and is a
+  #   symbolic link to a directory, follow the symlink and copy into the directory
+  #   it points to, instead of removing the symlink and creating a real directory in its place.
+  cp_flags="-a --keep-directory-symlink"
+else
+  # -L: always follow symbolic links in SOURCE
+  cp_flags="-Lr --preserve=all --no-preserve=link --keep-directory-symlink"
 fi

-# Process multiple input files
-IFS=";" read -ra input_files <<< "\$par_input"
-for file in "\${input_files[@]}"; do
-  # Check if the file exists before copying
-  if [[ -f "\$file" ]]; then
-
-    cp \${extra_params[@]} "\$file" "\$par_output/"
-    echo "Copied \$file to \$par_output/"
+# Process multiple input paths (files or directories)
+IFS=";" read -ra input_paths <<< "\$par_input"
+for path in "\${input_paths[@]}"; do
+  if [[ -e "\$path" ]] || [[ -L "\$path" ]]; then
+    cp \$cp_flags "\$path" "\$par_output/"
+    echo "Copied \$path to \$par_output/"
  else
-    echo "Warning: Input file \$file does not exist, skipping"
+    echo "Warning: Input path \$path does not exist, skipping"
  fi
 done
 VIASHMAIN
--- a/target/executable/sync_resources/.config.vsh.yaml
+++ b/target/executable/sync_resources/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "sync_resources"
-version: "v0.3.0"
+version: "v0.3.2"
 authors:
 - name: "Robrecht Cannoodt"
  roles:
@@ -174,7 +174,7 @@ engines:
  id: "docker"
  image: "alpine:3"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.0"
+  target_tag: "v0.3.2"
  namespace_separator: "/"
  setup:
  - type: "apk"
@@ -196,13 +196,12 @@ build_info:
  engine: "docker|native"
  output: "target/executable/sync_resources"
  executable: "target/executable/sync_resources/sync_resources"
-  viash_version: "0.9.4"
-  git_commit: "a1801c5139bbcda244e06affa66d16f7abd5e124"
+  viash_version: "0.9.7"
+  git_commit: "7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9"
  git_remote: "https://github.com/viash-hub/craftbox"
-  git_tag: "v0.1.0-11-ga1801c5"
 package_config:
  name: "craftbox"
-  version: "v0.3.0"
+  version: "v0.3.2"
  summary: "A collection of custom-tailored scripts and applied utilities built with\
    \ Viash.\n"
  description: "`craftbox` is a curated collection of custom scripts and utilities\
@@ -218,14 +217,14 @@ package_config:
    \ to ensure dependency management and a consistent, reproducible runtime environment.\n\
    \    * Unit tested where applicable to ensure components function as expected.\n"
  info: null
-  viash_version: "0.9.4"
+  viash_version: "0.9.7"
  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 := 'v0.3.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
  keywords:
  - "scripts"
  - "custom"
--- a/target/executable/sync_resources/sync_resources
+++ b/target/executable/sync_resources/sync_resources
@@ -1,8 +1,8 @@
 #!/usr/bin/env bash

-# sync_resources v0.3.0
+# sync_resources v0.3.2
 # 
-# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.7 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -455,10 +455,10 @@ RUN rclone config create s3 s3 anonymous=true
 RUN rclone config create gs gcs anonymous=true
 LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component sync_resources"
-LABEL org.opencontainers.image.created="2025-08-28T13:48:16Z"
+LABEL org.opencontainers.image.created="2026-03-03T15:11:58Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/craftbox"
-LABEL org.opencontainers.image.revision="a1801c5139bbcda244e06affa66d16f7abd5e124"
-LABEL org.opencontainers.image.version="v0.3.0"
+LABEL org.opencontainers.image.revision="7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9"
+LABEL org.opencontainers.image.version="v0.3.2"

 VIASHDOCKER
  fi
@@ -575,7 +575,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "sync_resources v0.3.0"
+  echo "sync_resources v0.3.2"
  echo ""
  echo "Sync a Viash package's test resources to the local filesystem based on the"
  echo "the \`.info.test_resources\` field in the \`_viash.yaml\` file. This is useful for"
@@ -654,7 +654,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "sync_resources v0.3.0"
+            echo "sync_resources v0.3.2"
            exit
            ;;
        --input)
@@ -801,7 +801,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/craftbox/sync_resources:v0.3.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/craftbox/sync_resources:v0.3.2'
  fi

  # print dockerfile
--- a/target/executable/untar/.config.vsh.yaml
+++ b/target/executable/untar/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "untar"
-version: "v0.3.0"
+version: "v0.3.2"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -164,7 +164,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.0"
+  target_tag: "v0.3.2"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -181,13 +181,12 @@ build_info:
  engine: "docker|native"
  output: "target/executable/untar"
  executable: "target/executable/untar/untar"
-  viash_version: "0.9.4"
-  git_commit: "a1801c5139bbcda244e06affa66d16f7abd5e124"
+  viash_version: "0.9.7"
+  git_commit: "7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9"
  git_remote: "https://github.com/viash-hub/craftbox"
-  git_tag: "v0.1.0-11-ga1801c5"
 package_config:
  name: "craftbox"
-  version: "v0.3.0"
+  version: "v0.3.2"
  summary: "A collection of custom-tailored scripts and applied utilities built with\
    \ Viash.\n"
  description: "`craftbox` is a curated collection of custom scripts and utilities\
@@ -203,14 +202,14 @@ package_config:
    \ to ensure dependency management and a consistent, reproducible runtime environment.\n\
    \    * Unit tested where applicable to ensure components function as expected.\n"
  info: null
-  viash_version: "0.9.4"
+  viash_version: "0.9.7"
  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 := 'v0.3.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
  keywords:
  - "scripts"
  - "custom"
--- a/target/executable/untar/untar
+++ b/target/executable/untar/untar
@@ -1,8 +1,8 @@
 #!/usr/bin/env bash

-# untar v0.3.0
+# untar v0.3.2
 # 
-# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.7 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -455,10 +455,10 @@ RUN apt-get update && \

 LABEL org.opencontainers.image.authors="Dries Schaumont, Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component untar"
-LABEL org.opencontainers.image.created="2025-08-28T13:48:16Z"
+LABEL org.opencontainers.image.created="2026-03-03T15:11:57Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/craftbox"
-LABEL org.opencontainers.image.revision="a1801c5139bbcda244e06affa66d16f7abd5e124"
-LABEL org.opencontainers.image.version="v0.3.0"
+LABEL org.opencontainers.image.revision="7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9"
+LABEL org.opencontainers.image.version="v0.3.2"

 VIASHDOCKER
  fi
@@ -575,7 +575,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "untar v0.3.0"
+  echo "untar v0.3.2"
  echo ""
  echo "Unpack a .tar file. When the contents of the .tar file is just a single"
  echo "directory,"
@@ -646,7 +646,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "untar v0.3.0"
+            echo "untar v0.3.2"
            exit
            ;;
        --input)
@@ -776,7 +776,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/craftbox/untar:v0.3.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/craftbox/untar:v0.3.2'
  fi

  # print dockerfile
--- a/target/nextflow/check_disk_space/.config.vsh.yaml
+++ b/target/nextflow/check_disk_space/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "check_disk_space"
-version: "v0.3.0"
+version: "v0.3.2"
 argument_groups:
 - name: "Inputs"
  arguments:
@@ -144,7 +144,7 @@ engines:
  id: "docker"
  image: "bash:latest"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.0"
+  target_tag: "v0.3.2"
  namespace_separator: "/"
  entrypoint: []
  cmd: null
@@ -156,13 +156,12 @@ build_info:
  engine: "docker|native"
  output: "target/nextflow/check_disk_space"
  executable: "target/nextflow/check_disk_space/main.nf"
-  viash_version: "0.9.4"
-  git_commit: "a1801c5139bbcda244e06affa66d16f7abd5e124"
+  viash_version: "0.9.7"
+  git_commit: "7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9"
  git_remote: "https://github.com/viash-hub/craftbox"
-  git_tag: "v0.1.0-11-ga1801c5"
 package_config:
  name: "craftbox"
-  version: "v0.3.0"
+  version: "v0.3.2"
  summary: "A collection of custom-tailored scripts and applied utilities built with\
    \ Viash.\n"
  description: "`craftbox` is a curated collection of custom scripts and utilities\
@@ -178,14 +177,14 @@ package_config:
    \ to ensure dependency management and a consistent, reproducible runtime environment.\n\
    \    * Unit tested where applicable to ensure components function as expected.\n"
  info: null
-  viash_version: "0.9.4"
+  viash_version: "0.9.7"
  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 := 'v0.3.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
  keywords:
  - "scripts"
  - "custom"
--- a/target/nextflow/check_disk_space/main.nf
+++ b/target/nextflow/check_disk_space/main.nf
@@ -1,6 +1,6 @@
-// check_disk_space v0.3.0
+// check_disk_space v0.3.2
 // 
-// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.7 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -1350,47 +1350,42 @@ def readCsv(file_path) {
  def splitRegex = java.util.regex.Pattern.compile(''',(?=(?:[^"]*"[^"]*")*[^"]*$)''')
  def removeQuote = java.util.regex.Pattern.compile('''"(.*)"''')

-  def br = java.nio.file.Files.newBufferedReader(inputFile)
+  java.nio.file.Files.newBufferedReader(inputFile).withCloseable { br ->
+    def row = 0
+    def header = null
+    def line

-  def row = -1
-  def header = null
-  while (br.ready() && header == null) {
-    def line = br.readLine()
-    row++
-    if (!line.startsWith("#")) {
-      header = splitRegex.split(line, -1).collect{field ->
-        m = removeQuote.matcher(field)
-        m.find() ? m.replaceFirst('$1') : field
-      }
-    }
-  }
-  assert header != null: "CSV file should contain a header"
-
-  while (br.ready()) {
-    def line = br.readLine()
-    row++
-    if (line == null) {
-      br.close()
-      break
-    }
-
-    if (!line.startsWith("#")) {
-      def predata = splitRegex.split(line, -1)
-      def data = predata.collect{field ->
-        if (field == "") {
-          return null
-        }
-        def m = removeQuote.matcher(field)
-        if (m.find()) {
-          return m.replaceFirst('$1')
-        } else {
-          return field
+    while (header == null && (line = br.readLine()) != null) {
+      if (!line.startsWith("#")) {
+        header = splitRegex.split(line, -1).collect { field ->
+          def m = removeQuote.matcher(field)
+          m.find() ? m.replaceFirst('$1') : field
        }
      }
-      assert header.size() == data.size(): "Row $row should contain the same number as fields as the header"
-      
-      def dataMap = [header, data].transpose().collectEntries().findAll{it.value != null}
-      output.add(dataMap)
+      row++
+    }
+    assert header != null : "CSV file should contain a header"
+
+    while ((line = br.readLine()) != null) {
+      row++
+      if (!line.startsWith("#")) {
+        def predata = splitRegex.split(line, -1)
+        def data = predata.collect { field ->
+          if (field == "") {
+            return null
+          }
+          def m = removeQuote.matcher(field)
+          if (m.find()) {
+            return m.replaceFirst('$1')
+          } else {
+            return field
+          }
+        }
+        assert header.size() == data.size() : "Row $row should contain the same number as fields as the header"
+
+        def dataMap = [header, data].transpose().collectEntries().findAll { it.value != null }
+        output.add(dataMap)
+      }
    }
  }

@@ -1706,10 +1701,25 @@ process publishFilesProc {
  ]
    .transpose()
    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
+      def infileString = infile.toString()
+      def outfileString = outfile.toString()
+      if (infileString != outfileString) {
+        /* Trailing slashes are removed from both the source and destination arguments.
+           From source arguments, this is useful when a source argument may have a trailing slash
+           and specify a symbolic link to a directory. Without removing the slash, cp will dereference
+           the symbolic link. 
+           See https://www.gnu.org/software/coreutils/manual/html_node/Trailing-slashes.html#Trailing-slashes-1
+
+           For the destination path addding a trailing slash is a problem when publishing directories: 
+           it requires the destination directory to exist. This fails because we only create the parent
+           directories first.
+        */
+        def regexTrailingSlashes = ~/\/+$/
+        def infileNoTrailingSlash = infileString - regexTrailingSlashes
+        def outfileNoTrailingSlash = outfileString - regexTrailingSlashes
        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+          "[ -d \"\$(dirname '${outfileNoTrailingSlash}')\" ] || mkdir -p \"\$(dirname '${outfileNoTrailingSlash}')\"",
+          "cp -a '${infileNoTrailingSlash}' '${outfileNoTrailingSlash}'"
        ]
      } else {
        // no need to copy if infile is the same as outfile
@@ -3031,7 +3041,7 @@ meta = [
  "resources_dir": moduleDir.toRealPath().normalize(),
  "config": processConfig(readJsonBlob('''{
  "name" : "check_disk_space",
-  "version" : "v0.3.0",
+  "version" : "v0.3.2",
  "argument_groups" : [
    {
      "name" : "Inputs",
@@ -3202,7 +3212,7 @@ meta = [
      "id" : "docker",
      "image" : "bash:latest",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.3.0",
+      "target_tag" : "v0.3.2",
      "namespace_separator" : "/"
    },
    {
@@ -3215,24 +3225,23 @@ meta = [
    "runner" : "nextflow",
    "engine" : "docker|native",
    "output" : "target/nextflow/check_disk_space",
-    "viash_version" : "0.9.4",
-    "git_commit" : "a1801c5139bbcda244e06affa66d16f7abd5e124",
-    "git_remote" : "https://github.com/viash-hub/craftbox",
-    "git_tag" : "v0.1.0-11-ga1801c5"
+    "viash_version" : "0.9.7",
+    "git_commit" : "7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9",
+    "git_remote" : "https://github.com/viash-hub/craftbox"
  },
  "package_config" : {
    "name" : "craftbox",
-    "version" : "v0.3.0",
+    "version" : "v0.3.2",
    "summary" : "A collection of custom-tailored scripts and applied utilities built with Viash.\n",
    "description" : "`craftbox` is a curated collection of custom scripts and utilities designed to tackle context-specific tasks.\n\nEmphasizing the Viash principles, `craftbox` components aim for **reusability**, **reproducibility**, and adherence to **best practices**. Key features generally include:\n\n* **Standalone & Nextflow Ready:** Components are built to run directly via the command line or be smoothly integrated into Nextflow workflows.\n* **Custom Implementations:** Contains scripts and tools developed for particular tasks that may not be found in broader collections.\n* **High Quality Standards (promoted by Viash):**\n    * Clear documentation for components and their parameters.\n    * Full exposure of underlying script/tool arguments for fine-grained control.\n    * Containerized (Docker) to ensure dependency management and a consistent, reproducible runtime environment.\n    * Unit tested where applicable to ensure components function as expected.\n",
-    "viash_version" : "0.9.4",
+    "viash_version" : "0.9.7",
    "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 := 'v0.3.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
    ],
    "keywords" : [
      "scripts",
@@ -3686,7 +3695,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/craftbox/check_disk_space",
-    "tag" : "v0.3.0"
+    "tag" : "v0.3.2"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/check_disk_space/nextflow.config
+++ b/target/nextflow/check_disk_space/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'check_disk_space'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.3.0'
+  version = 'v0.3.2'
  description = 'Check for available disk space on the system.\n\nThis component is only useful when working with persistent storage environments\nwhere all workflow steps execute on the same instance or share the same\nstorage volume. That is, running thus component on e.g. AWS Batch or\nother cloud-based systems will not work as expected, since each step\ncan run on a different instance and resources will not be shared.\n\nFor distributed environments, consider integrating resource checks directly\ninto the components that will actually consume the storage, rather than\nusing this standalone check.\n'
 }

--- a/target/nextflow/concat_text/.config.vsh.yaml
+++ b/target/nextflow/concat_text/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "concat_text"
-version: "v0.3.0"
+version: "v0.3.2"
 authors:
 - name: "Toni Verbeiren"
  roles:
@@ -26,6 +26,22 @@ authors:
    - name: "Data Intuitive"
      href: "https://www.data-intuitive.com"
      role: "Data Scientist"
+- name: "Robrecht Cannoodt"
+  roles:
+  - "contributor"
+  info:
+    links:
+      email: "robrecht@data-intuitive.com"
+      github: "rcannood"
+      orcid: "0000-0003-3641-729X"
+      linkedin: "robrechtcannoodt"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Science Engineer"
+    - name: "Open Problems"
+      href: "https://openproblems.bio"
+      role: "Core Member"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -34,7 +50,7 @@ argument_groups:
    description: "A list of (gzipped) text files."
    info: null
    example:
-    - "input?.txt.gz"
+    - "input.txt.gz"
    must_exist: true
    create_parent: true
    required: true
@@ -50,7 +66,7 @@ argument_groups:
    direction: "input"
  - type: "file"
    name: "--output"
-    description: "File to write the output to, optionally gzipped."
+    description: "File to write the output to, potentially gzipped."
    info: null
    example:
    - "output.txt"
@@ -64,7 +80,7 @@ resources:
 - type: "bash_script"
  path: "script.sh"
  is_executable: true
-summary: "Concatenate a number of text files"
+summary: "Concatenate multiple (possibly gzipped) text files"
 description: "Concatenate a number of text files, handle gzipped text files gracefully\
  \ and\noptionally gzip the output text file.\n\nThis component is useful for concatening\
  \ fastq files from different lanes, for instance.\n"
@@ -73,9 +89,8 @@ test_resources:
  path: "test.sh"
  is_executable: true
 info:
-  improvements: "This component could be improved in 2 ways:\n  1. Allow for a mix\
-    \ of zipped and plain input files\n  2. Allow to specify a compression algorithm\
-    \ for the output\n"
+  improvements: "This component could be improved:\n  1. Allow to specify a compression\
+    \ algorithm for the output\n"
 status: "enabled"
 scope:
  image: "public"
@@ -156,7 +171,7 @@ engines:
  id: "docker"
  image: "alpine:latest"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.0"
+  target_tag: "v0.3.2"
  namespace_separator: "/"
  setup:
  - type: "apk"
@@ -174,13 +189,12 @@ build_info:
  engine: "docker|native"
  output: "target/nextflow/concat_text"
  executable: "target/nextflow/concat_text/main.nf"
-  viash_version: "0.9.4"
-  git_commit: "a1801c5139bbcda244e06affa66d16f7abd5e124"
+  viash_version: "0.9.7"
+  git_commit: "7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9"
  git_remote: "https://github.com/viash-hub/craftbox"
-  git_tag: "v0.1.0-11-ga1801c5"
 package_config:
  name: "craftbox"
-  version: "v0.3.0"
+  version: "v0.3.2"
  summary: "A collection of custom-tailored scripts and applied utilities built with\
    \ Viash.\n"
  description: "`craftbox` is a curated collection of custom scripts and utilities\
@@ -196,14 +210,14 @@ package_config:
    \ to ensure dependency management and a consistent, reproducible runtime environment.\n\
    \    * Unit tested where applicable to ensure components function as expected.\n"
  info: null
-  viash_version: "0.9.4"
+  viash_version: "0.9.7"
  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 := 'v0.3.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
  keywords:
  - "scripts"
  - "custom"
--- a/target/nextflow/concat_text/main.nf
+++ b/target/nextflow/concat_text/main.nf
@@ -1,6 +1,6 @@
-// concat_text v0.3.0
+// concat_text v0.3.2
 // 
-// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.7 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -12,6 +12,7 @@
 // Component authors:
 //  * Toni Verbeiren (author, maintainer)
 //  * Dries Schaumont (reviewer)
+//  * Robrecht Cannoodt (contributor)

 ////////////////////////////
 // VDSL3 helper functions //
@@ -1354,47 +1355,42 @@ def readCsv(file_path) {
  def splitRegex = java.util.regex.Pattern.compile(''',(?=(?:[^"]*"[^"]*")*[^"]*$)''')
  def removeQuote = java.util.regex.Pattern.compile('''"(.*)"''')

-  def br = java.nio.file.Files.newBufferedReader(inputFile)
+  java.nio.file.Files.newBufferedReader(inputFile).withCloseable { br ->
+    def row = 0
+    def header = null
+    def line

-  def row = -1
-  def header = null
-  while (br.ready() && header == null) {
-    def line = br.readLine()
-    row++
-    if (!line.startsWith("#")) {
-      header = splitRegex.split(line, -1).collect{field ->
-        m = removeQuote.matcher(field)
-        m.find() ? m.replaceFirst('$1') : field
-      }
-    }
-  }
-  assert header != null: "CSV file should contain a header"
-
-  while (br.ready()) {
-    def line = br.readLine()
-    row++
-    if (line == null) {
-      br.close()
-      break
-    }
-
-    if (!line.startsWith("#")) {
-      def predata = splitRegex.split(line, -1)
-      def data = predata.collect{field ->
-        if (field == "") {
-          return null
-        }
-        def m = removeQuote.matcher(field)
-        if (m.find()) {
-          return m.replaceFirst('$1')
-        } else {
-          return field
+    while (header == null && (line = br.readLine()) != null) {
+      if (!line.startsWith("#")) {
+        header = splitRegex.split(line, -1).collect { field ->
+          def m = removeQuote.matcher(field)
+          m.find() ? m.replaceFirst('$1') : field
        }
      }
-      assert header.size() == data.size(): "Row $row should contain the same number as fields as the header"
-      
-      def dataMap = [header, data].transpose().collectEntries().findAll{it.value != null}
-      output.add(dataMap)
+      row++
+    }
+    assert header != null : "CSV file should contain a header"
+
+    while ((line = br.readLine()) != null) {
+      row++
+      if (!line.startsWith("#")) {
+        def predata = splitRegex.split(line, -1)
+        def data = predata.collect { field ->
+          if (field == "") {
+            return null
+          }
+          def m = removeQuote.matcher(field)
+          if (m.find()) {
+            return m.replaceFirst('$1')
+          } else {
+            return field
+          }
+        }
+        assert header.size() == data.size() : "Row $row should contain the same number as fields as the header"
+
+        def dataMap = [header, data].transpose().collectEntries().findAll { it.value != null }
+        output.add(dataMap)
+      }
    }
  }

@@ -1710,10 +1706,25 @@ process publishFilesProc {
  ]
    .transpose()
    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
+      def infileString = infile.toString()
+      def outfileString = outfile.toString()
+      if (infileString != outfileString) {
+        /* Trailing slashes are removed from both the source and destination arguments.
+           From source arguments, this is useful when a source argument may have a trailing slash
+           and specify a symbolic link to a directory. Without removing the slash, cp will dereference
+           the symbolic link. 
+           See https://www.gnu.org/software/coreutils/manual/html_node/Trailing-slashes.html#Trailing-slashes-1
+
+           For the destination path addding a trailing slash is a problem when publishing directories: 
+           it requires the destination directory to exist. This fails because we only create the parent
+           directories first.
+        */
+        def regexTrailingSlashes = ~/\/+$/
+        def infileNoTrailingSlash = infileString - regexTrailingSlashes
+        def outfileNoTrailingSlash = outfileString - regexTrailingSlashes
        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+          "[ -d \"\$(dirname '${outfileNoTrailingSlash}')\" ] || mkdir -p \"\$(dirname '${outfileNoTrailingSlash}')\"",
+          "cp -a '${infileNoTrailingSlash}' '${outfileNoTrailingSlash}'"
        ]
      } else {
        // no need to copy if infile is the same as outfile
@@ -3035,7 +3046,7 @@ meta = [
  "resources_dir": moduleDir.toRealPath().normalize(),
  "config": processConfig(readJsonBlob('''{
  "name" : "concat_text",
-  "version" : "v0.3.0",
+  "version" : "v0.3.2",
  "authors" : [
    {
      "name" : "Toni Verbeiren",
@@ -3077,6 +3088,32 @@ meta = [
          }
        ]
      }
+    },
+    {
+      "name" : "Robrecht Cannoodt",
+      "roles" : [
+        "contributor"
+      ],
+      "info" : {
+        "links" : {
+          "email" : "robrecht@data-intuitive.com",
+          "github" : "rcannood",
+          "orcid" : "0000-0003-3641-729X",
+          "linkedin" : "robrechtcannoodt"
+        },
+        "organizations" : [
+          {
+            "name" : "Data Intuitive",
+            "href" : "https://www.data-intuitive.com",
+            "role" : "Data Science Engineer"
+          },
+          {
+            "name" : "Open Problems",
+            "href" : "https://openproblems.bio",
+            "role" : "Core Member"
+          }
+        ]
+      }
    }
  ],
  "argument_groups" : [
@@ -3088,7 +3125,7 @@ meta = [
          "name" : "--input",
          "description" : "A list of (gzipped) text files.",
          "example" : [
-            "input?.txt.gz"
+            "input.txt.gz"
          ],
          "must_exist" : true,
          "create_parent" : true,
@@ -3111,7 +3148,7 @@ meta = [
        {
          "type" : "file",
          "name" : "--output",
-          "description" : "File to write the output to, optionally gzipped.",
+          "description" : "File to write the output to, potentially gzipped.",
          "example" : [
            "output.txt"
          ],
@@ -3132,7 +3169,7 @@ meta = [
      "is_executable" : true
    }
  ],
-  "summary" : "Concatenate a number of text files",
+  "summary" : "Concatenate multiple (possibly gzipped) text files",
  "description" : "Concatenate a number of text files, handle gzipped text files gracefully and\noptionally gzip the output text file.\n\nThis component is useful for concatening fastq files from different lanes, for instance.\n",
  "test_resources" : [
    {
@@ -3142,7 +3179,7 @@ meta = [
    }
  ],
  "info" : {
-    "improvements" : "This component could be improved in 2 ways:\n  1. Allow for a mix of zipped and plain input files\n  2. Allow to specify a compression algorithm for the output\n"
+    "improvements" : "This component could be improved:\n  1. Allow to specify a compression algorithm for the output\n"
  },
  "status" : "enabled",
  "scope" : {
@@ -3238,7 +3275,7 @@ meta = [
      "id" : "docker",
      "image" : "alpine:latest",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.3.0",
+      "target_tag" : "v0.3.2",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3261,24 +3298,23 @@ meta = [
    "runner" : "nextflow",
    "engine" : "docker|native",
    "output" : "target/nextflow/concat_text",
-    "viash_version" : "0.9.4",
-    "git_commit" : "a1801c5139bbcda244e06affa66d16f7abd5e124",
-    "git_remote" : "https://github.com/viash-hub/craftbox",
-    "git_tag" : "v0.1.0-11-ga1801c5"
+    "viash_version" : "0.9.7",
+    "git_commit" : "7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9",
+    "git_remote" : "https://github.com/viash-hub/craftbox"
  },
  "package_config" : {
    "name" : "craftbox",
-    "version" : "v0.3.0",
+    "version" : "v0.3.2",
    "summary" : "A collection of custom-tailored scripts and applied utilities built with Viash.\n",
    "description" : "`craftbox` is a curated collection of custom scripts and utilities designed to tackle context-specific tasks.\n\nEmphasizing the Viash principles, `craftbox` components aim for **reusability**, **reproducibility**, and adherence to **best practices**. Key features generally include:\n\n* **Standalone & Nextflow Ready:** Components are built to run directly via the command line or be smoothly integrated into Nextflow workflows.\n* **Custom Implementations:** Contains scripts and tools developed for particular tasks that may not be found in broader collections.\n* **High Quality Standards (promoted by Viash):**\n    * Clear documentation for components and their parameters.\n    * Full exposure of underlying script/tool arguments for fine-grained control.\n    * Containerized (Docker) to ensure dependency management and a consistent, reproducible runtime environment.\n    * Unit tested where applicable to ensure components function as expected.\n",
-    "viash_version" : "0.9.4",
+    "viash_version" : "0.9.7",
    "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 := 'v0.3.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
    ],
    "keywords" : [
      "scripts",
@@ -3305,6 +3341,10 @@ def innerWorkflowFactory(args) {
  def rawScript = '''set -e
 tempscript=".viash_script.sh"
 cat > "$tempscript" << VIASHMAIN
+#!/usr/bin/env bash
+
+set -eo pipefail
+
 ## VIASH START
 # The following code has been auto-generated by Viash.
 $( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "${VIASH_PAR_INPUT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_input='&'#" ; else echo "# par_input="; fi )
@@ -3330,40 +3370,62 @@ $( if [ ! -z ${VIASH_META_MEMORY_TIB+x} ]; then echo "${VIASH_META_MEMORY_TIB}"
 $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_memory_pib='&'#" ; else echo "# meta_memory_pib="; fi )

 ## VIASH END
-#!/usr/bin/env bash

-set -euo pipefail
-
-TMPDIR=\\$(mktemp -d "\\$meta_temp_dir/concat_text-XXXXXX")
-function clean_up {
-  [[ -d "\\$TMPDIR" ]] && rm -r "\\$TMPDIR"
+# --- Function to check for GZIP format using the 'file' command ---
+is_gzipped() {
+    # Ensure the file exists and is not empty before checking
+    if [ ! -s "\\$1" ]; then
+        return 1
+    fi
+    # Get the MIME type of the file. The '-b' option omits the filename from the output.
+    local mime_type
+    mime_type=\\$(file -b --mime-type "\\$1")
+    
+    # Check if the MIME type corresponds to gzip.
+    # application/gzip is standard, while application/x-gzip is also commonly seen.
+    if [[ "\\$mime_type" == "application/gzip" || "\\$mime_type" == "application/x-gzip" ]]; then
+        return 0 # 0 indicates success (true in bash)
+    else
+        return 1 # 1 indicates failure (false in bash)
+    fi
 }
-trap clean_up EXIT

-par_input="\\$(echo "\\$par_input" | tr ';' ' ')"
+# Read the ;-separated file paths from the input variable into an array
+IFS=";" read -ra input_files <<< "\\$par_input"

-echo -n ">> Check if input is gzipped... "
-set +eo pipefail
-file \\$par_input | grep -q 'gzip'
-is_zipped="\\$?"
-set -euo pipefail
-[[ "\\$is_zipped" == "0" ]] && echo "yes" || echo "no"
+# Process the files if the array contains any paths
+if [ \\${#input_files[@]} -gt 0 ] && [ -n "\\${input_files[0]}" ]; then

-if [[ "\\$is_zipped" == "0" ]]; then
-  echo ">> zcat gzipped files"
-  zcat \\$par_input > \\$TMPDIR/contents
+    # Ensure the output file is empty before we start
+    > "\\$par_output"
+
+    echo "Processing files for -> \\$par_output"
+
+    # Create a subshell for the loop to group all cat/zcat output.
+    (
+        for file in "\\${input_files[@]}"; do
+            if [ -z "\\$file" ]; then continue; fi # Skip empty entries in the array
+
+            if is_gzipped "\\$file"; then
+                zcat "\\$file"
+            else
+                cat "\\$file"
+            fi
+        done
+    ) | if [ "\\$par_compress_output" = "true" ]; then
+        # If compression is enabled, pipe the entire stream to gzip
+        gzip -c >> "\\$par_output"
+    else
+        # Otherwise, just redirect the stream to the plain text file
+        cat >> "\\$par_output"
+    fi
+
+    echo "Finished creating \\$par_output."
 else
-  echo ">> cat plain files"
-  cat \\$par_input > \\$TMPDIR/contents
+    echo "No input files provided in \\\\\\$par_input. Exiting."
 fi

-if [ "\\$par_gzip_output" == true ]; then
-  echo ">> Zip output file"
-  gzip \\$TMPDIR/contents
-  mv \\$TMPDIR/contents.gz \\$par_output
-else
-  mv \\$TMPDIR/contents \\$par_output
-fi
+echo "Script finished successfully."
 VIASHMAIN
 bash "$tempscript"
 '''
@@ -3746,7 +3808,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/craftbox/concat_text",
-    "tag" : "v0.3.0"
+    "tag" : "v0.3.2"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/concat_text/nextflow.config
+++ b/target/nextflow/concat_text/nextflow.config
@@ -2,9 +2,9 @@ manifest {
  name = 'concat_text'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.3.0'
+  version = 'v0.3.2'
  description = 'Concatenate a number of text files, handle gzipped text files gracefully and\noptionally gzip the output text file.\n\nThis component is useful for concatening fastq files from different lanes, for instance.\n'
-  author = 'Toni Verbeiren, Dries Schaumont'
+  author = 'Toni Verbeiren, Dries Schaumont, Robrecht Cannoodt'
 }

 process.container = 'nextflow/bash:latest'
--- a/target/nextflow/concat_text/nextflow_schema.json
+++ b/target/nextflow/concat_text/nextflow_schema.json
@@ -17,7 +17,7 @@
          "format": "path",
          "exists": true,
          "description": "A list of (gzipped) text files.",
-          "help_text": "Type: `file`, multiple: `True`, required, direction: `input`, example: `[\"input?.txt.gz\"]`. "
+          "help_text": "Type: `file`, multiple: `True`, required, direction: `input`, example: `[\"input.txt.gz\"]`. "
        }
      }
    },
@@ -35,7 +35,7 @@
        "output": {
          "type": "string",
          "format": "path",
-          "description": "File to write the output to, optionally gzipped.",
+          "description": "File to write the output to, potentially gzipped.",
          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output.txt\"`, direction: `output`, example: `\"output.txt\"`. ",
          "default": "$id.$key.output.txt"
        }
--- a/target/nextflow/csv2fasta/.config.vsh.yaml
+++ b/target/nextflow/csv2fasta/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "csv2fasta"
-version: "v0.3.0"
+version: "v0.3.2"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -227,7 +227,7 @@ engines:
  id: "docker"
  image: "python:slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.0"
+  target_tag: "v0.3.2"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -256,13 +256,12 @@ build_info:
  engine: "docker|native"
  output: "target/nextflow/csv2fasta"
  executable: "target/nextflow/csv2fasta/main.nf"
-  viash_version: "0.9.4"
-  git_commit: "a1801c5139bbcda244e06affa66d16f7abd5e124"
+  viash_version: "0.9.7"
+  git_commit: "7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9"
  git_remote: "https://github.com/viash-hub/craftbox"
-  git_tag: "v0.1.0-11-ga1801c5"
 package_config:
  name: "craftbox"
-  version: "v0.3.0"
+  version: "v0.3.2"
  summary: "A collection of custom-tailored scripts and applied utilities built with\
    \ Viash.\n"
  description: "`craftbox` is a curated collection of custom scripts and utilities\
@@ -278,14 +277,14 @@ package_config:
    \ to ensure dependency management and a consistent, reproducible runtime environment.\n\
    \    * Unit tested where applicable to ensure components function as expected.\n"
  info: null
-  viash_version: "0.9.4"
+  viash_version: "0.9.7"
  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 := 'v0.3.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
  keywords:
  - "scripts"
  - "custom"
--- a/target/nextflow/csv2fasta/main.nf
+++ b/target/nextflow/csv2fasta/main.nf
@@ -1,6 +1,6 @@
-// csv2fasta v0.3.0
+// csv2fasta v0.3.2
 // 
-// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.7 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -1354,47 +1354,42 @@ def readCsv(file_path) {
  def splitRegex = java.util.regex.Pattern.compile(''',(?=(?:[^"]*"[^"]*")*[^"]*$)''')
  def removeQuote = java.util.regex.Pattern.compile('''"(.*)"''')

-  def br = java.nio.file.Files.newBufferedReader(inputFile)
+  java.nio.file.Files.newBufferedReader(inputFile).withCloseable { br ->
+    def row = 0
+    def header = null
+    def line

-  def row = -1
-  def header = null
-  while (br.ready() && header == null) {
-    def line = br.readLine()
-    row++
-    if (!line.startsWith("#")) {
-      header = splitRegex.split(line, -1).collect{field ->
-        m = removeQuote.matcher(field)
-        m.find() ? m.replaceFirst('$1') : field
-      }
-    }
-  }
-  assert header != null: "CSV file should contain a header"
-
-  while (br.ready()) {
-    def line = br.readLine()
-    row++
-    if (line == null) {
-      br.close()
-      break
-    }
-
-    if (!line.startsWith("#")) {
-      def predata = splitRegex.split(line, -1)
-      def data = predata.collect{field ->
-        if (field == "") {
-          return null
-        }
-        def m = removeQuote.matcher(field)
-        if (m.find()) {
-          return m.replaceFirst('$1')
-        } else {
-          return field
+    while (header == null && (line = br.readLine()) != null) {
+      if (!line.startsWith("#")) {
+        header = splitRegex.split(line, -1).collect { field ->
+          def m = removeQuote.matcher(field)
+          m.find() ? m.replaceFirst('$1') : field
        }
      }
-      assert header.size() == data.size(): "Row $row should contain the same number as fields as the header"
-      
-      def dataMap = [header, data].transpose().collectEntries().findAll{it.value != null}
-      output.add(dataMap)
+      row++
+    }
+    assert header != null : "CSV file should contain a header"
+
+    while ((line = br.readLine()) != null) {
+      row++
+      if (!line.startsWith("#")) {
+        def predata = splitRegex.split(line, -1)
+        def data = predata.collect { field ->
+          if (field == "") {
+            return null
+          }
+          def m = removeQuote.matcher(field)
+          if (m.find()) {
+            return m.replaceFirst('$1')
+          } else {
+            return field
+          }
+        }
+        assert header.size() == data.size() : "Row $row should contain the same number as fields as the header"
+
+        def dataMap = [header, data].transpose().collectEntries().findAll { it.value != null }
+        output.add(dataMap)
+      }
    }
  }

@@ -1710,10 +1705,25 @@ process publishFilesProc {
  ]
    .transpose()
    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
+      def infileString = infile.toString()
+      def outfileString = outfile.toString()
+      if (infileString != outfileString) {
+        /* Trailing slashes are removed from both the source and destination arguments.
+           From source arguments, this is useful when a source argument may have a trailing slash
+           and specify a symbolic link to a directory. Without removing the slash, cp will dereference
+           the symbolic link. 
+           See https://www.gnu.org/software/coreutils/manual/html_node/Trailing-slashes.html#Trailing-slashes-1
+
+           For the destination path addding a trailing slash is a problem when publishing directories: 
+           it requires the destination directory to exist. This fails because we only create the parent
+           directories first.
+        */
+        def regexTrailingSlashes = ~/\/+$/
+        def infileNoTrailingSlash = infileString - regexTrailingSlashes
+        def outfileNoTrailingSlash = outfileString - regexTrailingSlashes
        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+          "[ -d \"\$(dirname '${outfileNoTrailingSlash}')\" ] || mkdir -p \"\$(dirname '${outfileNoTrailingSlash}')\"",
+          "cp -a '${infileNoTrailingSlash}' '${outfileNoTrailingSlash}'"
        ]
      } else {
        // no need to copy if infile is the same as outfile
@@ -3035,7 +3045,7 @@ meta = [
  "resources_dir": moduleDir.toRealPath().normalize(),
  "config": processConfig(readJsonBlob('''{
  "name" : "csv2fasta",
-  "version" : "v0.3.0",
+  "version" : "v0.3.2",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -3310,7 +3320,7 @@ meta = [
      "id" : "docker",
      "image" : "python:slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.3.0",
+      "target_tag" : "v0.3.2",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3351,24 +3361,23 @@ meta = [
    "runner" : "nextflow",
    "engine" : "docker|native",
    "output" : "target/nextflow/csv2fasta",
-    "viash_version" : "0.9.4",
-    "git_commit" : "a1801c5139bbcda244e06affa66d16f7abd5e124",
-    "git_remote" : "https://github.com/viash-hub/craftbox",
-    "git_tag" : "v0.1.0-11-ga1801c5"
+    "viash_version" : "0.9.7",
+    "git_commit" : "7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9",
+    "git_remote" : "https://github.com/viash-hub/craftbox"
  },
  "package_config" : {
    "name" : "craftbox",
-    "version" : "v0.3.0",
+    "version" : "v0.3.2",
    "summary" : "A collection of custom-tailored scripts and applied utilities built with Viash.\n",
    "description" : "`craftbox` is a curated collection of custom scripts and utilities designed to tackle context-specific tasks.\n\nEmphasizing the Viash principles, `craftbox` components aim for **reusability**, **reproducibility**, and adherence to **best practices**. Key features generally include:\n\n* **Standalone & Nextflow Ready:** Components are built to run directly via the command line or be smoothly integrated into Nextflow workflows.\n* **Custom Implementations:** Contains scripts and tools developed for particular tasks that may not be found in broader collections.\n* **High Quality Standards (promoted by Viash):**\n    * Clear documentation for components and their parameters.\n    * Full exposure of underlying script/tool arguments for fine-grained control.\n    * Containerized (Docker) to ensure dependency management and a consistent, reproducible runtime environment.\n    * Unit tested where applicable to ensure components function as expected.\n",
-    "viash_version" : "0.9.4",
+    "viash_version" : "0.9.7",
    "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 := 'v0.3.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
    ],
    "keywords" : [
      "scripts",
@@ -3912,7 +3921,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/craftbox/csv2fasta",
-    "tag" : "v0.3.0"
+    "tag" : "v0.3.2"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/csv2fasta/nextflow.config
+++ b/target/nextflow/csv2fasta/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'csv2fasta'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.3.0'
+  version = 'v0.3.2'
  description = 'Convert two columns from a CSV file to FASTA entries. The CSV file can\ncontain an optional header and each row (other than the header) becomes\na single FASTA record. One of the two columns will be used as the names\nfor the FASTA entries, while the other become the sequences. The sequences\ncolumn must only contain characters that are valid IUPAC notation for \nnucleotides or a group thereof (wildcard characters).\n'
  author = 'Dries Schaumont, Robrecht Cannoodt'
 }
--- a/target/nextflow/move_files_to_directory/.config.vsh.yaml
+++ b/target/nextflow/move_files_to_directory/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "move_files_to_directory"
-version: "v0.3.0"
+version: "v0.3.2"
 authors:
 - name: "Dorien Roosen"
  roles:
@@ -14,11 +14,12 @@ authors:
      href: "https://www.data-intuitive.com"
      role: "Data Scientist"
 argument_groups:
- name: "Arguments"
+- name: "Inputs"
  arguments:
  - type: "file"
    name: "--input"
-    description: "Paths of the files that will be copied into the output directory."
+    description: "Paths of the files or directories that will be copied into the output\
+      \ directory."
    info: null
    must_exist: true
    create_parent: true
@@ -26,9 +27,11 @@ argument_groups:
    direction: "input"
    multiple: true
    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
  - type: "file"
    name: "--output"
-    description: "Path to output directory"
+    description: "Path to output directory."
    info: null
    must_exist: true
    create_parent: true
@@ -36,20 +39,22 @@ argument_groups:
    direction: "output"
    multiple: false
    multiple_sep: ";"
+- name: "Options"
+  arguments:
  - type: "boolean_true"
    name: "--keep_symbolic_links"
-    alternatives:
-    - "-d"
-    description: "Preserve symbolic links."
+    description: "When set, symbolic links are preserved as symbolic links in the\
+      \ output directory. By default, symbolic links are dereferenced and the target\
+      \ file is copied."
    info: null
    direction: "input"
 resources:
 - type: "bash_script"
  path: "script.sh"
  is_executable: true
-summary: "Publish one or multiple files to the same directory"
-description: "This component copies one or multiple files to the same destination\
-  \ directory, creating the output directory if it doesn't exist."
+summary: "Publish one or multiple files or directories to the same output directory."
+description: "This component copies one or multiple files or directories\nto the same\
+  \ destination directory, creating the output directory if it doesn't\nexist.\n"
 test_resources:
 - type: "bash_script"
  path: "test.sh"
@@ -135,7 +140,7 @@ engines:
  id: "docker"
  image: "debian:latest"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.0"
+  target_tag: "v0.3.2"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -146,19 +151,20 @@ engines:
  cmd: null
 - type: "native"
  id: "native"
+- type: "native"
+  id: "native"
 build_info:
  config: "src/move_files_to_directory/config.vsh.yaml"
  runner: "nextflow"
-  engine: "docker|native"
+  engine: "docker|native|native"
  output: "target/nextflow/move_files_to_directory"
  executable: "target/nextflow/move_files_to_directory/main.nf"
-  viash_version: "0.9.4"
-  git_commit: "a1801c5139bbcda244e06affa66d16f7abd5e124"
+  viash_version: "0.9.7"
+  git_commit: "7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9"
  git_remote: "https://github.com/viash-hub/craftbox"
-  git_tag: "v0.1.0-11-ga1801c5"
 package_config:
  name: "craftbox"
-  version: "v0.3.0"
+  version: "v0.3.2"
  summary: "A collection of custom-tailored scripts and applied utilities built with\
    \ Viash.\n"
  description: "`craftbox` is a curated collection of custom scripts and utilities\
@@ -174,14 +180,14 @@ package_config:
    \ to ensure dependency management and a consistent, reproducible runtime environment.\n\
    \    * Unit tested where applicable to ensure components function as expected.\n"
  info: null
-  viash_version: "0.9.4"
+  viash_version: "0.9.7"
  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 := 'v0.3.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
  keywords:
  - "scripts"
  - "custom"
--- a/target/nextflow/move_files_to_directory/main.nf
+++ b/target/nextflow/move_files_to_directory/main.nf
@@ -1,6 +1,6 @@
-// move_files_to_directory v0.3.0
+// move_files_to_directory v0.3.2
 // 
-// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.7 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -1353,47 +1353,42 @@ def readCsv(file_path) {
  def splitRegex = java.util.regex.Pattern.compile(''',(?=(?:[^"]*"[^"]*")*[^"]*$)''')
  def removeQuote = java.util.regex.Pattern.compile('''"(.*)"''')

-  def br = java.nio.file.Files.newBufferedReader(inputFile)
+  java.nio.file.Files.newBufferedReader(inputFile).withCloseable { br ->
+    def row = 0
+    def header = null
+    def line

-  def row = -1
-  def header = null
-  while (br.ready() && header == null) {
-    def line = br.readLine()
-    row++
-    if (!line.startsWith("#")) {
-      header = splitRegex.split(line, -1).collect{field ->
-        m = removeQuote.matcher(field)
-        m.find() ? m.replaceFirst('$1') : field
-      }
-    }
-  }
-  assert header != null: "CSV file should contain a header"
-
-  while (br.ready()) {
-    def line = br.readLine()
-    row++
-    if (line == null) {
-      br.close()
-      break
-    }
-
-    if (!line.startsWith("#")) {
-      def predata = splitRegex.split(line, -1)
-      def data = predata.collect{field ->
-        if (field == "") {
-          return null
-        }
-        def m = removeQuote.matcher(field)
-        if (m.find()) {
-          return m.replaceFirst('$1')
-        } else {
-          return field
+    while (header == null && (line = br.readLine()) != null) {
+      if (!line.startsWith("#")) {
+        header = splitRegex.split(line, -1).collect { field ->
+          def m = removeQuote.matcher(field)
+          m.find() ? m.replaceFirst('$1') : field
        }
      }
-      assert header.size() == data.size(): "Row $row should contain the same number as fields as the header"
-      
-      def dataMap = [header, data].transpose().collectEntries().findAll{it.value != null}
-      output.add(dataMap)
+      row++
+    }
+    assert header != null : "CSV file should contain a header"
+
+    while ((line = br.readLine()) != null) {
+      row++
+      if (!line.startsWith("#")) {
+        def predata = splitRegex.split(line, -1)
+        def data = predata.collect { field ->
+          if (field == "") {
+            return null
+          }
+          def m = removeQuote.matcher(field)
+          if (m.find()) {
+            return m.replaceFirst('$1')
+          } else {
+            return field
+          }
+        }
+        assert header.size() == data.size() : "Row $row should contain the same number as fields as the header"
+
+        def dataMap = [header, data].transpose().collectEntries().findAll { it.value != null }
+        output.add(dataMap)
+      }
    }
  }

@@ -1709,10 +1704,25 @@ process publishFilesProc {
  ]
    .transpose()
    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
+      def infileString = infile.toString()
+      def outfileString = outfile.toString()
+      if (infileString != outfileString) {
+        /* Trailing slashes are removed from both the source and destination arguments.
+           From source arguments, this is useful when a source argument may have a trailing slash
+           and specify a symbolic link to a directory. Without removing the slash, cp will dereference
+           the symbolic link. 
+           See https://www.gnu.org/software/coreutils/manual/html_node/Trailing-slashes.html#Trailing-slashes-1
+
+           For the destination path addding a trailing slash is a problem when publishing directories: 
+           it requires the destination directory to exist. This fails because we only create the parent
+           directories first.
+        */
+        def regexTrailingSlashes = ~/\/+$/
+        def infileNoTrailingSlash = infileString - regexTrailingSlashes
+        def outfileNoTrailingSlash = outfileString - regexTrailingSlashes
        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+          "[ -d \"\$(dirname '${outfileNoTrailingSlash}')\" ] || mkdir -p \"\$(dirname '${outfileNoTrailingSlash}')\"",
+          "cp -a '${infileNoTrailingSlash}' '${outfileNoTrailingSlash}'"
        ]
      } else {
        // no need to copy if infile is the same as outfile
@@ -3034,7 +3044,7 @@ meta = [
  "resources_dir": moduleDir.toRealPath().normalize(),
  "config": processConfig(readJsonBlob('''{
  "name" : "move_files_to_directory",
-  "version" : "v0.3.0",
+  "version" : "v0.3.2",
  "authors" : [
    {
      "name" : "Dorien Roosen",
@@ -3059,37 +3069,44 @@ meta = [
  ],
  "argument_groups" : [
    {
-      "name" : "Arguments",
+      "name" : "Inputs",
      "arguments" : [
        {
          "type" : "file",
          "name" : "--input",
-          "description" : "Paths of the files that will be copied into the output directory.",
+          "description" : "Paths of the files or directories that will be copied into the output directory.",
          "must_exist" : true,
          "create_parent" : true,
          "required" : true,
          "direction" : "input",
          "multiple" : true,
          "multiple_sep" : ";"
-        },
+        }
+      ]
+    },
+    {
+      "name" : "Outputs",
+      "arguments" : [
        {
          "type" : "file",
          "name" : "--output",
-          "description" : "Path to output directory",
+          "description" : "Path to output directory.",
          "must_exist" : true,
          "create_parent" : true,
          "required" : true,
          "direction" : "output",
          "multiple" : false,
          "multiple_sep" : ";"
-        },
+        }
+      ]
+    },
+    {
+      "name" : "Options",
+      "arguments" : [
        {
          "type" : "boolean_true",
          "name" : "--keep_symbolic_links",
-          "alternatives" : [
-            "-d"
-          ],
-          "description" : "Preserve symbolic links.",
+          "description" : "When set, symbolic links are preserved as symbolic links in the output directory. By default, symbolic links are dereferenced and the target file is copied.",
          "direction" : "input"
        }
      ]
@@ -3102,8 +3119,8 @@ meta = [
      "is_executable" : true
    }
  ],
-  "summary" : "Publish one or multiple files to the same directory",
-  "description" : "This component copies one or multiple files to the same destination directory, creating the output directory if it doesn't exist.",
+  "summary" : "Publish one or multiple files or directories to the same output directory.",
+  "description" : "This component copies one or multiple files or directories\nto the same destination directory, creating the output directory if it doesn't\nexist.\n",
  "test_resources" : [
    {
      "type" : "bash_script",
@@ -3205,7 +3222,7 @@ meta = [
      "id" : "docker",
      "image" : "debian:latest",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.3.0",
+      "target_tag" : "v0.3.2",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3217,6 +3234,10 @@ meta = [
        }
      ]
    },
+    {
+      "type" : "native",
+      "id" : "native"
+    },
    {
      "type" : "native",
      "id" : "native"
@@ -3225,26 +3246,25 @@ meta = [
  "build_info" : {
    "config" : "/workdir/root/repo/src/move_files_to_directory/config.vsh.yaml",
    "runner" : "nextflow",
-    "engine" : "docker|native",
+    "engine" : "docker|native|native",
    "output" : "target/nextflow/move_files_to_directory",
-    "viash_version" : "0.9.4",
-    "git_commit" : "a1801c5139bbcda244e06affa66d16f7abd5e124",
-    "git_remote" : "https://github.com/viash-hub/craftbox",
-    "git_tag" : "v0.1.0-11-ga1801c5"
+    "viash_version" : "0.9.7",
+    "git_commit" : "7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9",
+    "git_remote" : "https://github.com/viash-hub/craftbox"
  },
  "package_config" : {
    "name" : "craftbox",
-    "version" : "v0.3.0",
+    "version" : "v0.3.2",
    "summary" : "A collection of custom-tailored scripts and applied utilities built with Viash.\n",
    "description" : "`craftbox` is a curated collection of custom scripts and utilities designed to tackle context-specific tasks.\n\nEmphasizing the Viash principles, `craftbox` components aim for **reusability**, **reproducibility**, and adherence to **best practices**. Key features generally include:\n\n* **Standalone & Nextflow Ready:** Components are built to run directly via the command line or be smoothly integrated into Nextflow workflows.\n* **Custom Implementations:** Contains scripts and tools developed for particular tasks that may not be found in broader collections.\n* **High Quality Standards (promoted by Viash):**\n    * Clear documentation for components and their parameters.\n    * Full exposure of underlying script/tool arguments for fine-grained control.\n    * Containerized (Docker) to ensure dependency management and a consistent, reproducible runtime environment.\n    * Unit tested where applicable to ensure components function as expected.\n",
-    "viash_version" : "0.9.4",
+    "viash_version" : "0.9.7",
    "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 := 'v0.3.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
    ],
    "keywords" : [
      "scripts",
@@ -3301,27 +3321,33 @@ $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}"

 ## VIASH END

-
 if [[ ! -d "\\$par_output" ]]; then
  mkdir -p "\\$par_output"
 fi

-extra_params=( )
-
-if [ "\\$par_keep_symbolic_links" == "true" ]; then
-  extra_params+=( "-d" )
+# Set copy flags based on options
+if [[ "\\$par_keep_symbolic_links" == "true" ]]; then
+  # -a implies -dR --preserve=all
+  # with -d: same as --no-dereference (and --preserve=links)
+  # and --no-dereference: never follow symbolic links in SOURCE
+  # and -R, -r, --recursive: copy directories recursively
+  # --keep-directory-symlink: if the destination already exists and is a
+  #   symbolic link to a directory, follow the symlink and copy into the directory
+  #   it points to, instead of removing the symlink and creating a real directory in its place.
+  cp_flags="-a --keep-directory-symlink"
+else
+  # -L: always follow symbolic links in SOURCE
+  cp_flags="-Lr --preserve=all --no-preserve=link --keep-directory-symlink"
 fi

-# Process multiple input files
-IFS=";" read -ra input_files <<< "\\$par_input"
-for file in "\\${input_files[@]}"; do
-  # Check if the file exists before copying
-  if [[ -f "\\$file" ]]; then
-
-    cp \\${extra_params[@]} "\\$file" "\\$par_output/"
-    echo "Copied \\$file to \\$par_output/"
+# Process multiple input paths (files or directories)
+IFS=";" read -ra input_paths <<< "\\$par_input"
+for path in "\\${input_paths[@]}"; do
+  if [[ -e "\\$path" ]] || [[ -L "\\$path" ]]; then
+    cp \\$cp_flags "\\$path" "\\$par_output/"
+    echo "Copied \\$path to \\$par_output/"
  else
-    echo "Warning: Input file \\$file does not exist, skipping"
+    echo "Warning: Input path \\$path does not exist, skipping"
  fi
 done
 VIASHMAIN
@@ -3706,7 +3732,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/craftbox/move_files_to_directory",
-    "tag" : "v0.3.0"
+    "tag" : "v0.3.2"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/move_files_to_directory/nextflow.config
+++ b/target/nextflow/move_files_to_directory/nextflow.config
@@ -2,8 +2,8 @@ manifest {
  name = 'move_files_to_directory'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.3.0'
-  description = 'This component copies one or multiple files to the same destination directory, creating the output directory if it doesn\'t exist.'
+  version = 'v0.3.2'
+  description = 'This component copies one or multiple files or directories\nto the same destination directory, creating the output directory if it doesn\'t\nexist.\n'
  author = 'Dorien Roosen'
 }

--- a/target/nextflow/move_files_to_directory/nextflow_schema.json
+++ b/target/nextflow/move_files_to_directory/nextflow_schema.json
@@ -1,11 +1,11 @@
 {
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "move_files_to_directory",
-  "description": "This component copies one or multiple files to the same destination directory, creating the output directory if it doesn't exist.",
+  "description": "This component copies one or multiple files or directories\nto the same destination directory, creating the output directory if it doesn't\nexist.\n",
  "type": "object",
  "$defs": {
-    "arguments": {
-      "title": "Arguments",
+    "inputs": {
+      "title": "Inputs",
      "type": "object",
      "description": "No description",
      "properties": {
@@ -16,19 +16,33 @@
          },
          "format": "path",
          "exists": true,
-          "description": "Paths of the files that will be copied into the output directory.",
+          "description": "Paths of the files or directories that will be copied into the output directory.",
          "help_text": "Type: `file`, multiple: `True`, required, direction: `input`. "
-        },
+        }
+      }
+    },
+    "outputs": {
+      "title": "Outputs",
+      "type": "object",
+      "description": "No description",
+      "properties": {
        "output": {
          "type": "string",
          "format": "path",
-          "description": "Path to output directory",
+          "description": "Path to output directory.",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output\"`, direction: `output`. ",
          "default": "$id.$key.output"
-        },
+        }
+      }
+    },
+    "options": {
+      "title": "Options",
+      "type": "object",
+      "description": "No description",
+      "properties": {
        "keep_symbolic_links": {
          "type": "boolean",
-          "description": "Preserve symbolic links.",
+          "description": "When set, symbolic links are preserved as symbolic links in the output directory",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        }
@@ -49,7 +63,13 @@
  },
  "allOf": [
    {
-      "$ref": "#/$defs/arguments"
+      "$ref": "#/$defs/inputs"
+    },
+    {
+      "$ref": "#/$defs/outputs"
+    },
+    {
+      "$ref": "#/$defs/options"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
--- a/target/nextflow/sync_resources/.config.vsh.yaml
+++ b/target/nextflow/sync_resources/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "sync_resources"
-version: "v0.3.0"
+version: "v0.3.2"
 authors:
 - name: "Robrecht Cannoodt"
  roles:
@@ -174,7 +174,7 @@ engines:
  id: "docker"
  image: "alpine:3"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.0"
+  target_tag: "v0.3.2"
  namespace_separator: "/"
  setup:
  - type: "apk"
@@ -196,13 +196,12 @@ build_info:
  engine: "docker|native"
  output: "target/nextflow/sync_resources"
  executable: "target/nextflow/sync_resources/main.nf"
-  viash_version: "0.9.4"
-  git_commit: "a1801c5139bbcda244e06affa66d16f7abd5e124"
+  viash_version: "0.9.7"
+  git_commit: "7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9"
  git_remote: "https://github.com/viash-hub/craftbox"
-  git_tag: "v0.1.0-11-ga1801c5"
 package_config:
  name: "craftbox"
-  version: "v0.3.0"
+  version: "v0.3.2"
  summary: "A collection of custom-tailored scripts and applied utilities built with\
    \ Viash.\n"
  description: "`craftbox` is a curated collection of custom scripts and utilities\
@@ -218,14 +217,14 @@ package_config:
    \ to ensure dependency management and a consistent, reproducible runtime environment.\n\
    \    * Unit tested where applicable to ensure components function as expected.\n"
  info: null
-  viash_version: "0.9.4"
+  viash_version: "0.9.7"
  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 := 'v0.3.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
  keywords:
  - "scripts"
  - "custom"
--- a/target/nextflow/sync_resources/main.nf
+++ b/target/nextflow/sync_resources/main.nf
@@ -1,6 +1,6 @@
-// sync_resources v0.3.0
+// sync_resources v0.3.2
 // 
-// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.7 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -1354,47 +1354,42 @@ def readCsv(file_path) {
  def splitRegex = java.util.regex.Pattern.compile(''',(?=(?:[^"]*"[^"]*")*[^"]*$)''')
  def removeQuote = java.util.regex.Pattern.compile('''"(.*)"''')

-  def br = java.nio.file.Files.newBufferedReader(inputFile)
+  java.nio.file.Files.newBufferedReader(inputFile).withCloseable { br ->
+    def row = 0
+    def header = null
+    def line

-  def row = -1
-  def header = null
-  while (br.ready() && header == null) {
-    def line = br.readLine()
-    row++
-    if (!line.startsWith("#")) {
-      header = splitRegex.split(line, -1).collect{field ->
-        m = removeQuote.matcher(field)
-        m.find() ? m.replaceFirst('$1') : field
-      }
-    }
-  }
-  assert header != null: "CSV file should contain a header"
-
-  while (br.ready()) {
-    def line = br.readLine()
-    row++
-    if (line == null) {
-      br.close()
-      break
-    }
-
-    if (!line.startsWith("#")) {
-      def predata = splitRegex.split(line, -1)
-      def data = predata.collect{field ->
-        if (field == "") {
-          return null
-        }
-        def m = removeQuote.matcher(field)
-        if (m.find()) {
-          return m.replaceFirst('$1')
-        } else {
-          return field
+    while (header == null && (line = br.readLine()) != null) {
+      if (!line.startsWith("#")) {
+        header = splitRegex.split(line, -1).collect { field ->
+          def m = removeQuote.matcher(field)
+          m.find() ? m.replaceFirst('$1') : field
        }
      }
-      assert header.size() == data.size(): "Row $row should contain the same number as fields as the header"
-      
-      def dataMap = [header, data].transpose().collectEntries().findAll{it.value != null}
-      output.add(dataMap)
+      row++
+    }
+    assert header != null : "CSV file should contain a header"
+
+    while ((line = br.readLine()) != null) {
+      row++
+      if (!line.startsWith("#")) {
+        def predata = splitRegex.split(line, -1)
+        def data = predata.collect { field ->
+          if (field == "") {
+            return null
+          }
+          def m = removeQuote.matcher(field)
+          if (m.find()) {
+            return m.replaceFirst('$1')
+          } else {
+            return field
+          }
+        }
+        assert header.size() == data.size() : "Row $row should contain the same number as fields as the header"
+
+        def dataMap = [header, data].transpose().collectEntries().findAll { it.value != null }
+        output.add(dataMap)
+      }
    }
  }

@@ -1710,10 +1705,25 @@ process publishFilesProc {
  ]
    .transpose()
    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
+      def infileString = infile.toString()
+      def outfileString = outfile.toString()
+      if (infileString != outfileString) {
+        /* Trailing slashes are removed from both the source and destination arguments.
+           From source arguments, this is useful when a source argument may have a trailing slash
+           and specify a symbolic link to a directory. Without removing the slash, cp will dereference
+           the symbolic link. 
+           See https://www.gnu.org/software/coreutils/manual/html_node/Trailing-slashes.html#Trailing-slashes-1
+
+           For the destination path addding a trailing slash is a problem when publishing directories: 
+           it requires the destination directory to exist. This fails because we only create the parent
+           directories first.
+        */
+        def regexTrailingSlashes = ~/\/+$/
+        def infileNoTrailingSlash = infileString - regexTrailingSlashes
+        def outfileNoTrailingSlash = outfileString - regexTrailingSlashes
        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+          "[ -d \"\$(dirname '${outfileNoTrailingSlash}')\" ] || mkdir -p \"\$(dirname '${outfileNoTrailingSlash}')\"",
+          "cp -a '${infileNoTrailingSlash}' '${outfileNoTrailingSlash}'"
        ]
      } else {
        // no need to copy if infile is the same as outfile
@@ -3035,7 +3045,7 @@ meta = [
  "resources_dir": moduleDir.toRealPath().normalize(),
  "config": processConfig(readJsonBlob('''{
  "name" : "sync_resources",
-  "version" : "v0.3.0",
+  "version" : "v0.3.2",
  "authors" : [
    {
      "name" : "Robrecht Cannoodt",
@@ -3263,7 +3273,7 @@ meta = [
      "id" : "docker",
      "image" : "alpine:3",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.3.0",
+      "target_tag" : "v0.3.2",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3293,24 +3303,23 @@ meta = [
    "runner" : "nextflow",
    "engine" : "docker|native",
    "output" : "target/nextflow/sync_resources",
-    "viash_version" : "0.9.4",
-    "git_commit" : "a1801c5139bbcda244e06affa66d16f7abd5e124",
-    "git_remote" : "https://github.com/viash-hub/craftbox",
-    "git_tag" : "v0.1.0-11-ga1801c5"
+    "viash_version" : "0.9.7",
+    "git_commit" : "7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9",
+    "git_remote" : "https://github.com/viash-hub/craftbox"
  },
  "package_config" : {
    "name" : "craftbox",
-    "version" : "v0.3.0",
+    "version" : "v0.3.2",
    "summary" : "A collection of custom-tailored scripts and applied utilities built with Viash.\n",
    "description" : "`craftbox` is a curated collection of custom scripts and utilities designed to tackle context-specific tasks.\n\nEmphasizing the Viash principles, `craftbox` components aim for **reusability**, **reproducibility**, and adherence to **best practices**. Key features generally include:\n\n* **Standalone & Nextflow Ready:** Components are built to run directly via the command line or be smoothly integrated into Nextflow workflows.\n* **Custom Implementations:** Contains scripts and tools developed for particular tasks that may not be found in broader collections.\n* **High Quality Standards (promoted by Viash):**\n    * Clear documentation for components and their parameters.\n    * Full exposure of underlying script/tool arguments for fine-grained control.\n    * Containerized (Docker) to ensure dependency management and a consistent, reproducible runtime environment.\n    * Unit tested where applicable to ensure components function as expected.\n",
-    "viash_version" : "0.9.4",
+    "viash_version" : "0.9.7",
    "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 := 'v0.3.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
    ],
    "keywords" : [
      "scripts",
@@ -3773,7 +3782,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/craftbox/sync_resources",
-    "tag" : "v0.3.0"
+    "tag" : "v0.3.2"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/sync_resources/nextflow.config
+++ b/target/nextflow/sync_resources/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'sync_resources'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.3.0'
+  version = 'v0.3.2'
  description = 'Sync a Viash package\'s test resources to the local filesystem based on the\nthe `.info.test_resources` field in the `_viash.yaml` file. This is useful for\ntesting and debugging purposes.\n'
  author = 'Robrecht Cannoodt, Dries Schaumont'
 }
--- a/target/nextflow/untar/.config.vsh.yaml
+++ b/target/nextflow/untar/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "untar"
-version: "v0.3.0"
+version: "v0.3.2"
 authors:
 - name: "Dries Schaumont"
  roles:
@@ -164,7 +164,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.0"
+  target_tag: "v0.3.2"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -181,13 +181,12 @@ build_info:
  engine: "docker|native"
  output: "target/nextflow/untar"
  executable: "target/nextflow/untar/main.nf"
-  viash_version: "0.9.4"
-  git_commit: "a1801c5139bbcda244e06affa66d16f7abd5e124"
+  viash_version: "0.9.7"
+  git_commit: "7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9"
  git_remote: "https://github.com/viash-hub/craftbox"
-  git_tag: "v0.1.0-11-ga1801c5"
 package_config:
  name: "craftbox"
-  version: "v0.3.0"
+  version: "v0.3.2"
  summary: "A collection of custom-tailored scripts and applied utilities built with\
    \ Viash.\n"
  description: "`craftbox` is a curated collection of custom scripts and utilities\
@@ -203,14 +202,14 @@ package_config:
    \ to ensure dependency management and a consistent, reproducible runtime environment.\n\
    \    * Unit tested where applicable to ensure components function as expected.\n"
  info: null
-  viash_version: "0.9.4"
+  viash_version: "0.9.7"
  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 := 'v0.3.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
  keywords:
  - "scripts"
  - "custom"
--- a/target/nextflow/untar/main.nf
+++ b/target/nextflow/untar/main.nf
@@ -1,6 +1,6 @@
-// untar v0.3.0
+// untar v0.3.2
 // 
-// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.7 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -1354,47 +1354,42 @@ def readCsv(file_path) {
  def splitRegex = java.util.regex.Pattern.compile(''',(?=(?:[^"]*"[^"]*")*[^"]*$)''')
  def removeQuote = java.util.regex.Pattern.compile('''"(.*)"''')

-  def br = java.nio.file.Files.newBufferedReader(inputFile)
+  java.nio.file.Files.newBufferedReader(inputFile).withCloseable { br ->
+    def row = 0
+    def header = null
+    def line

-  def row = -1
-  def header = null
-  while (br.ready() && header == null) {
-    def line = br.readLine()
-    row++
-    if (!line.startsWith("#")) {
-      header = splitRegex.split(line, -1).collect{field ->
-        m = removeQuote.matcher(field)
-        m.find() ? m.replaceFirst('$1') : field
-      }
-    }
-  }
-  assert header != null: "CSV file should contain a header"
-
-  while (br.ready()) {
-    def line = br.readLine()
-    row++
-    if (line == null) {
-      br.close()
-      break
-    }
-
-    if (!line.startsWith("#")) {
-      def predata = splitRegex.split(line, -1)
-      def data = predata.collect{field ->
-        if (field == "") {
-          return null
-        }
-        def m = removeQuote.matcher(field)
-        if (m.find()) {
-          return m.replaceFirst('$1')
-        } else {
-          return field
+    while (header == null && (line = br.readLine()) != null) {
+      if (!line.startsWith("#")) {
+        header = splitRegex.split(line, -1).collect { field ->
+          def m = removeQuote.matcher(field)
+          m.find() ? m.replaceFirst('$1') : field
        }
      }
-      assert header.size() == data.size(): "Row $row should contain the same number as fields as the header"
-      
-      def dataMap = [header, data].transpose().collectEntries().findAll{it.value != null}
-      output.add(dataMap)
+      row++
+    }
+    assert header != null : "CSV file should contain a header"
+
+    while ((line = br.readLine()) != null) {
+      row++
+      if (!line.startsWith("#")) {
+        def predata = splitRegex.split(line, -1)
+        def data = predata.collect { field ->
+          if (field == "") {
+            return null
+          }
+          def m = removeQuote.matcher(field)
+          if (m.find()) {
+            return m.replaceFirst('$1')
+          } else {
+            return field
+          }
+        }
+        assert header.size() == data.size() : "Row $row should contain the same number as fields as the header"
+
+        def dataMap = [header, data].transpose().collectEntries().findAll { it.value != null }
+        output.add(dataMap)
+      }
    }
  }

@@ -1710,10 +1705,25 @@ process publishFilesProc {
  ]
    .transpose()
    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
+      def infileString = infile.toString()
+      def outfileString = outfile.toString()
+      if (infileString != outfileString) {
+        /* Trailing slashes are removed from both the source and destination arguments.
+           From source arguments, this is useful when a source argument may have a trailing slash
+           and specify a symbolic link to a directory. Without removing the slash, cp will dereference
+           the symbolic link. 
+           See https://www.gnu.org/software/coreutils/manual/html_node/Trailing-slashes.html#Trailing-slashes-1
+
+           For the destination path addding a trailing slash is a problem when publishing directories: 
+           it requires the destination directory to exist. This fails because we only create the parent
+           directories first.
+        */
+        def regexTrailingSlashes = ~/\/+$/
+        def infileNoTrailingSlash = infileString - regexTrailingSlashes
+        def outfileNoTrailingSlash = outfileString - regexTrailingSlashes
        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+          "[ -d \"\$(dirname '${outfileNoTrailingSlash}')\" ] || mkdir -p \"\$(dirname '${outfileNoTrailingSlash}')\"",
+          "cp -a '${infileNoTrailingSlash}' '${outfileNoTrailingSlash}'"
        ]
      } else {
        // no need to copy if infile is the same as outfile
@@ -3035,7 +3045,7 @@ meta = [
  "resources_dir": moduleDir.toRealPath().normalize(),
  "config": processConfig(readJsonBlob('''{
  "name" : "untar",
-  "version" : "v0.3.0",
+  "version" : "v0.3.2",
  "authors" : [
    {
      "name" : "Dries Schaumont",
@@ -3250,7 +3260,7 @@ meta = [
      "id" : "docker",
      "image" : "debian:stable-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.3.0",
+      "target_tag" : "v0.3.2",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3272,24 +3282,23 @@ meta = [
    "runner" : "nextflow",
    "engine" : "docker|native",
    "output" : "target/nextflow/untar",
-    "viash_version" : "0.9.4",
-    "git_commit" : "a1801c5139bbcda244e06affa66d16f7abd5e124",
-    "git_remote" : "https://github.com/viash-hub/craftbox",
-    "git_tag" : "v0.1.0-11-ga1801c5"
+    "viash_version" : "0.9.7",
+    "git_commit" : "7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9",
+    "git_remote" : "https://github.com/viash-hub/craftbox"
  },
  "package_config" : {
    "name" : "craftbox",
-    "version" : "v0.3.0",
+    "version" : "v0.3.2",
    "summary" : "A collection of custom-tailored scripts and applied utilities built with Viash.\n",
    "description" : "`craftbox` is a curated collection of custom scripts and utilities designed to tackle context-specific tasks.\n\nEmphasizing the Viash principles, `craftbox` components aim for **reusability**, **reproducibility**, and adherence to **best practices**. Key features generally include:\n\n* **Standalone & Nextflow Ready:** Components are built to run directly via the command line or be smoothly integrated into Nextflow workflows.\n* **Custom Implementations:** Contains scripts and tools developed for particular tasks that may not be found in broader collections.\n* **High Quality Standards (promoted by Viash):**\n    * Clear documentation for components and their parameters.\n    * Full exposure of underlying script/tool arguments for fine-grained control.\n    * Containerized (Docker) to ensure dependency management and a consistent, reproducible runtime environment.\n    * Unit tested where applicable to ensure components function as expected.\n",
-    "viash_version" : "0.9.4",
+    "viash_version" : "0.9.7",
    "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 := 'v0.3.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
    ],
    "keywords" : [
      "scripts",
@@ -3763,7 +3772,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/craftbox/untar",
-    "tag" : "v0.3.0"
+    "tag" : "v0.3.2"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/untar/nextflow.config
+++ b/target/nextflow/untar/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'untar'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.3.0'
+  version = 'v0.3.2'
  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'
  author = 'Dries Schaumont, Robrecht Cannoodt'
 }
Author	SHA1	Message	Date
CI	4ccb4240e0	Build branch craftbox/v0.3 with version v0.3.2 to craftbox on branch v0.3 (7d520dc) Build pipeline: viash-hub.craftbox.v0.3.2-tpktm Source commit: `7d520dc76c` Source message: Bump version to v0.3.2	2026-03-03 15:18:58 +00:00
CI	6c59599998	Build branch craftbox/v0.3 with version v0.3.1 to craftbox on branch v0.3 (4acf73e) Build pipeline: viash-hub.craftbox.v0.3.1-6qf24 Source commit: `4acf73e025` Source message: Bump version to v0.3.1	2025-11-20 15:23:55 +00:00