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

CHANGELOG.md

@@ -1,3 +1,13 @@
+# 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

README.md

@@ -43,7 +43,7 @@ Viash components in craftbox can be run in various ways:
 
 ``` mermaid lang="mermaid
 flowchart TD
-    A[craftbox v0.3.1] --> 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=v0.3.1&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@v0.3.1/concat_rtext -- --help
+viash run vsh://craftbox@v0.3.2/concat_rtext -- --help
 
-viash run vsh://craftbox@v0.3.1/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 v0.3.1 \
+  -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@v0.3.1
+    repository: vsh://craftbox@v0.3.2
 ```
 
 **Tip:** See the [Viash

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$version else "v0.3.1"
+ver <- if (!is.null(package$version)) package$version else "v0.3.2"
 comp <- "concat_rtext"
 ```
 # 🪡📦 `r pkg`

_viash.yaml

@@ -1,5 +1,5 @@
 name: craftbox
-version: v0.3.1
+version: v0.3.2
 summary: |
   A collection of custom-tailored scripts and applied utilities built with Viash.
 description: |
@@ -19,7 +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

nextflow.config

@@ -1,6 +1,6 @@
 manifest {
   name = "craftbox"
-  version = "v0.3.1"
+  version = "v0.3.2"
   defaultBranch = "main"
   nextflowVersion = "!>=20.12.1-edge"
 }

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
+summary: Publish one or multiple files or directories to the same output 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
+  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"
+argument_groups:
-    type: file
+  - name: Inputs
-    direction: input
+    arguments:
-    required: true
+      - name: "--input"
-    multiple: true
+        type: file
-    description: Paths of the files that will be copied into the output directory.
+        direction: input
-  - name: "--output"
+        required: true
-    type: file
+        multiple: true
-    direction: output
+        description: Paths of the files or directories that will be copied into the output directory.
-    required: true
+  - name: Outputs
-    description: Path to output directory
+    arguments:
-  - name: "--keep_symbolic_links"
+      - name: "--output"
-    alternatives: [-d]
+        type: file
-    type: boolean_true
+        direction: output
-    description: Preserve symbolic links.
+        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
+  - type: docker
-  image: debian:latest
+    image: debian:latest
-  setup:
+    setup:
       - type: apt
-        packages: [procps]
+        packages:
+          - procps
+  - type: native
 
 runners:
-- type: executable
+  - type: executable
-- type: nextflow
+  - type: nextflow

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=( )
+# Set copy flags based on options
-
+if [[ "$par_keep_symbolic_links" == "true" ]]; then
-if [ "$par_keep_symbolic_links" == "true" ]; then
+  # -a implies -dR --preserve=all
-  extra_params+=( "-d" )
+  # 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
+# Process multiple input paths (files or directories)
-IFS=";" read -ra input_files <<< "$par_input"
+IFS=";" read -ra input_paths <<< "$par_input"
-for file in "${input_files[@]}"; do
+for path in "${input_paths[@]}"; do
-  # Check if the file exists before copying
+  if [[ -e "$path" ]] || [[ -L "$path" ]]; then
-  if [[ -f "$file" ]]; then
+    cp $cp_flags "$path" "$par_output/"
-
+    echo "Copied $path to $par_output/"
-    cp ${extra_params[@]} "$file" "$par_output/"
-    echo "Copied $file to $par_output/"
   else
-    echo "Warning: Input file $file does not exist, skipping"
+    echo "Warning: Input path $path does not exist, skipping"
   fi
 done

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

target/executable/check_disk_space/.config.vsh.yaml

@@ -1,5 +1,5 @@
 name: "check_disk_space"
-version: "v0.3.1"
+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: "v0.3.1"
+  target_tag: "v0.3.2"
   namespace_separator: "/"
   entrypoint: []
   cmd: null
@@ -156,12 +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"
+  viash_version: "0.9.7"
-  git_commit: "4acf73e0255554766186f4016986782c0d25c309"
+  git_commit: "7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9"
   git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
   name: "craftbox"
-  version: "v0.3.1"
+  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\
@@ -177,14 +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 := 'v0.3.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
   keywords:
   - "scripts"
   - "custom"

target/executable/check_disk_space/check_disk_space

@@ -1,8 +1,8 @@
 #!/usr/bin/env bash
 
-# check_disk_space v0.3.1
+# 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="2025-11-20T15:16:24Z"
+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="4acf73e0255554766186f4016986782c0d25c309"
+LABEL org.opencontainers.image.revision="7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9"
-LABEL org.opencontainers.image.version="v0.3.1"
+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 v0.3.1"
+  echo "check_disk_space v0.3.2"
   echo ""
   echo "Check for available disk space on the system."
   echo ""
@@ -648,7 +648,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "check_disk_space v0.3.1"
+            echo "check_disk_space v0.3.2"
             exit
             ;;
         --tmp_space_required)
@@ -783,7 +783,7 @@ if [[ "$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:v0.3.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/craftbox/check_disk_space:v0.3.2'
   fi
 
   # print dockerfile

target/executable/concat_text/.config.vsh.yaml

@@ -1,5 +1,5 @@
 name: "concat_text"
-version: "v0.3.1"
+version: "v0.3.2"
 authors:
 - name: "Toni Verbeiren"
   roles:
@@ -171,7 +171,7 @@ engines:
   id: "docker"
   image: "alpine:latest"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.1"
+  target_tag: "v0.3.2"
   namespace_separator: "/"
   setup:
   - type: "apk"
@@ -189,12 +189,12 @@ build_info:
   engine: "docker|native"
   output: "target/executable/concat_text"
   executable: "target/executable/concat_text/concat_text"
-  viash_version: "0.9.4"
+  viash_version: "0.9.7"
-  git_commit: "4acf73e0255554766186f4016986782c0d25c309"
+  git_commit: "7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9"
   git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
   name: "craftbox"
-  version: "v0.3.1"
+  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\
@@ -210,14 +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 := 'v0.3.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
   keywords:
   - "scripts"
   - "custom"

target/executable/concat_text/concat_text

@@ -1,8 +1,8 @@
 #!/usr/bin/env bash
 
-# concat_text v0.3.1
+# 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.
 # 
@@ -454,10 +454,10 @@ RUN apk add --no-cache bash procps file
 
 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="2025-11-20T15:16:24Z"
+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="4acf73e0255554766186f4016986782c0d25c309"
+LABEL org.opencontainers.image.revision="7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9"
-LABEL org.opencontainers.image.version="v0.3.1"
+LABEL org.opencontainers.image.version="v0.3.2"
 
 VIASHDOCKER
   fi
@@ -574,7 +574,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "concat_text v0.3.1"
+  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."
@@ -645,7 +645,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "concat_text v0.3.1"
+            echo "concat_text v0.3.2"
             exit
             ;;
         --input)
@@ -769,7 +769,7 @@ if [[ "$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:v0.3.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/craftbox/concat_text:v0.3.2'
   fi
 
   # print dockerfile

target/executable/csv2fasta/.config.vsh.yaml

@@ -1,5 +1,5 @@
 name: "csv2fasta"
-version: "v0.3.1"
+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: "v0.3.1"
+  target_tag: "v0.3.2"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -256,12 +256,12 @@ build_info:
   engine: "docker|native"
   output: "target/executable/csv2fasta"
   executable: "target/executable/csv2fasta/csv2fasta"
-  viash_version: "0.9.4"
+  viash_version: "0.9.7"
-  git_commit: "4acf73e0255554766186f4016986782c0d25c309"
+  git_commit: "7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9"
   git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
   name: "craftbox"
-  version: "v0.3.1"
+  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\
@@ -277,14 +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 := 'v0.3.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
   keywords:
   - "scripts"
   - "custom"

target/executable/csv2fasta/csv2fasta

@@ -1,8 +1,8 @@
 #!/usr/bin/env bash
 
-# csv2fasta v0.3.1
+# 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="2025-11-20T15:16:24Z"
+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="4acf73e0255554766186f4016986782c0d25c309"
+LABEL org.opencontainers.image.revision="7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9"
-LABEL org.opencontainers.image.version="v0.3.1"
+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 v0.3.1"
+  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 [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "csv2fasta v0.3.1"
+            echo "csv2fasta v0.3.2"
             exit
             ;;
         --input)
@@ -879,7 +879,7 @@ if [[ "$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:v0.3.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/craftbox/csv2fasta:v0.3.2'
   fi
 
   # print dockerfile

target/executable/move_files_to_directory/.config.vsh.yaml

@@ -1,5 +1,5 @@
 name: "move_files_to_directory"
-version: "v0.3.1"
+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:
+    description: "When set, symbolic links are preserved as symbolic links in the\
-    - "-d"
+      \ output directory. By default, symbolic links are dereferenced and the target\
-    description: "Preserve symbolic links."
+      \ 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"
+summary: "Publish one or multiple files or directories to the same output directory."
-description: "This component copies one or multiple files to the same destination\
+description: "This component copies one or multiple files or directories\nto the same\
-  \ directory, creating the output directory if it doesn't exist."
+  \ 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: "v0.3.1"
+  target_tag: "v0.3.2"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -146,18 +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"
+  viash_version: "0.9.7"
-  git_commit: "4acf73e0255554766186f4016986782c0d25c309"
+  git_commit: "7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9"
   git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
   name: "craftbox"
-  version: "v0.3.1"
+  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\
@@ -173,14 +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 := 'v0.3.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
   keywords:
   - "scripts"
   - "custom"

target/executable/move_files_to_directory/move_files_to_directory

@@ -1,8 +1,8 @@
 #!/usr/bin/env bash
 
-# move_files_to_directory v0.3.1
+# 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="2025-11-20T15:16:24Z"
+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="4acf73e0255554766186f4016986782c0d25c309"
+LABEL org.opencontainers.image.revision="7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9"
-LABEL org.opencontainers.image.version="v0.3.1"
+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 v0.3.1"
+  echo "move_files_to_directory v0.3.2"
   echo ""
-  echo "This component copies one or multiple files to the same destination directory,"
+  echo "This component copies one or multiple files or directories"
-  echo "creating the output directory if it doesn't exist."
+  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 v0.3.1"
+            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:v0.3.1'
+    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=( )
+# Set copy flags based on options
-
+if [[ "\$par_keep_symbolic_links" == "true" ]]; then
-if [ "\$par_keep_symbolic_links" == "true" ]; then
+  # -a implies -dR --preserve=all
-  extra_params+=( "-d" )
+  # 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
+# Process multiple input paths (files or directories)
-IFS=";" read -ra input_files <<< "\$par_input"
+IFS=";" read -ra input_paths <<< "\$par_input"
-for file in "\${input_files[@]}"; do
+for path in "\${input_paths[@]}"; do
-  # Check if the file exists before copying
+  if [[ -e "\$path" ]] || [[ -L "\$path" ]]; then
-  if [[ -f "\$file" ]]; then
+    cp \$cp_flags "\$path" "\$par_output/"
-
+    echo "Copied \$path to \$par_output/"
-    cp \${extra_params[@]} "\$file" "\$par_output/"
-    echo "Copied \$file 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

target/executable/sync_resources/.config.vsh.yaml

@@ -1,5 +1,5 @@
 name: "sync_resources"
-version: "v0.3.1"
+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: "v0.3.1"
+  target_tag: "v0.3.2"
   namespace_separator: "/"
   setup:
   - type: "apk"
@@ -196,12 +196,12 @@ build_info:
   engine: "docker|native"
   output: "target/executable/sync_resources"
   executable: "target/executable/sync_resources/sync_resources"
-  viash_version: "0.9.4"
+  viash_version: "0.9.7"
-  git_commit: "4acf73e0255554766186f4016986782c0d25c309"
+  git_commit: "7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9"
   git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
   name: "craftbox"
-  version: "v0.3.1"
+  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\
@@ -217,14 +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 := 'v0.3.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
   keywords:
   - "scripts"
   - "custom"

target/executable/sync_resources/sync_resources

@@ -1,8 +1,8 @@
 #!/usr/bin/env bash
 
-# sync_resources v0.3.1
+# 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="2025-11-20T15:16:24Z"
+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="4acf73e0255554766186f4016986782c0d25c309"
+LABEL org.opencontainers.image.revision="7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9"
-LABEL org.opencontainers.image.version="v0.3.1"
+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 v0.3.1"
+  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 [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "sync_resources v0.3.1"
+            echo "sync_resources v0.3.2"
             exit
             ;;
         --input)
@@ -801,7 +801,7 @@ if [[ "$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:v0.3.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/craftbox/sync_resources:v0.3.2'
   fi
 
   # print dockerfile

target/executable/untar/.config.vsh.yaml

@@ -1,5 +1,5 @@
 name: "untar"
-version: "v0.3.1"
+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: "v0.3.1"
+  target_tag: "v0.3.2"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -181,12 +181,12 @@ build_info:
   engine: "docker|native"
   output: "target/executable/untar"
   executable: "target/executable/untar/untar"
-  viash_version: "0.9.4"
+  viash_version: "0.9.7"
-  git_commit: "4acf73e0255554766186f4016986782c0d25c309"
+  git_commit: "7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9"
   git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
   name: "craftbox"
-  version: "v0.3.1"
+  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\
@@ -202,14 +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 := 'v0.3.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
   keywords:
   - "scripts"
   - "custom"

target/executable/untar/untar

@@ -1,8 +1,8 @@
 #!/usr/bin/env bash
 
-# untar v0.3.1
+# 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="2025-11-20T15:16:24Z"
+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="4acf73e0255554766186f4016986782c0d25c309"
+LABEL org.opencontainers.image.revision="7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9"
-LABEL org.opencontainers.image.version="v0.3.1"
+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 v0.3.1"
+  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 [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "untar v0.3.1"
+            echo "untar v0.3.2"
             exit
             ;;
         --input)
@@ -776,7 +776,7 @@ if [[ "$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:v0.3.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/craftbox/untar:v0.3.2'
   fi
 
   # print dockerfile

target/nextflow/check_disk_space/.config.vsh.yaml

@@ -1,5 +1,5 @@
 name: "check_disk_space"
-version: "v0.3.1"
+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: "v0.3.1"
+  target_tag: "v0.3.2"
   namespace_separator: "/"
   entrypoint: []
   cmd: null
@@ -156,12 +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"
+  viash_version: "0.9.7"
-  git_commit: "4acf73e0255554766186f4016986782c0d25c309"
+  git_commit: "7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9"
   git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
   name: "craftbox"
-  version: "v0.3.1"
+  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\
@@ -177,14 +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 := 'v0.3.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
   keywords:
   - "scripts"
   - "custom"

target/nextflow/check_disk_space/main.nf

@@ -1,6 +1,6 @@
-// check_disk_space v0.3.1
+// 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
+    while (header == null && (line = br.readLine()) != null) {
-  def header = null
+      if (!line.startsWith("#")) {
-  while (br.ready() && header == null) {
+        header = splitRegex.split(line, -1).collect { field ->
-    def line = br.readLine()
+          def m = removeQuote.matcher(field)
-    row++
+          m.find() ? m.replaceFirst('$1') : field
-    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
         }
       }
-      assert header.size() == data.size(): "Row $row should contain the same number as fields as the header"
+      row++
-      
+    }
-      def dataMap = [header, data].transpose().collectEntries().findAll{it.value != null}
+    assert header != null : "CSV file should contain a header"
-      output.add(dataMap)
+
+    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 '${outfile.toString()}')\"",
+          "[ -d \"\$(dirname '${outfileNoTrailingSlash}')\" ] || mkdir -p \"\$(dirname '${outfileNoTrailingSlash}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+          "cp -a '${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" : "v0.3.1",
+  "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" : "v0.3.1",
+      "target_tag" : "v0.3.2",
       "namespace_separator" : "/"
     },
     {
@@ -3215,23 +3225,23 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/check_disk_space",
-    "viash_version" : "0.9.4",
+    "viash_version" : "0.9.7",
-    "git_commit" : "4acf73e0255554766186f4016986782c0d25c309",
+    "git_commit" : "7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9",
     "git_remote" : "https://github.com/viash-hub/craftbox"
   },
   "package_config" : {
     "name" : "craftbox",
-    "version" : "v0.3.1",
+    "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 := 'v0.3.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
     ],
     "keywords" : [
       "scripts",
@@ -3685,7 +3695,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/craftbox/check_disk_space",
-    "tag" : "v0.3.1"
+    "tag" : "v0.3.2"
   },
   "tag" : "$id"
 }'''),

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 = 'v0.3.1'
+  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'
 }
 

target/nextflow/concat_text/.config.vsh.yaml

@@ -1,5 +1,5 @@
 name: "concat_text"
-version: "v0.3.1"
+version: "v0.3.2"
 authors:
 - name: "Toni Verbeiren"
   roles:
@@ -171,7 +171,7 @@ engines:
   id: "docker"
   image: "alpine:latest"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.3.1"
+  target_tag: "v0.3.2"
   namespace_separator: "/"
   setup:
   - type: "apk"
@@ -189,12 +189,12 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/concat_text"
   executable: "target/nextflow/concat_text/main.nf"
-  viash_version: "0.9.4"
+  viash_version: "0.9.7"
-  git_commit: "4acf73e0255554766186f4016986782c0d25c309"
+  git_commit: "7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9"
   git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
   name: "craftbox"
-  version: "v0.3.1"
+  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\
@@ -210,14 +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 := 'v0.3.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
   keywords:
   - "scripts"
   - "custom"

target/nextflow/concat_text/main.nf

@@ -1,6 +1,6 @@
-// concat_text v0.3.1
+// 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.
 // 
@@ -1355,47 +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
+    while (header == null && (line = br.readLine()) != null) {
-  def header = null
+      if (!line.startsWith("#")) {
-  while (br.ready() && header == null) {
+        header = splitRegex.split(line, -1).collect { field ->
-    def line = br.readLine()
+          def m = removeQuote.matcher(field)
-    row++
+          m.find() ? m.replaceFirst('$1') : field
-    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
         }
       }
-      assert header.size() == data.size(): "Row $row should contain the same number as fields as the header"
+      row++
-      
+    }
-      def dataMap = [header, data].transpose().collectEntries().findAll{it.value != null}
+    assert header != null : "CSV file should contain a header"
-      output.add(dataMap)
+
+    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)
+      }
     }
   }
 
@@ -1711,10 +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 '${outfile.toString()}')\"",
+          "[ -d \"\$(dirname '${outfileNoTrailingSlash}')\" ] || mkdir -p \"\$(dirname '${outfileNoTrailingSlash}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+          "cp -a '${infileNoTrailingSlash}' '${outfileNoTrailingSlash}'"
         ]
       } else {
         // no need to copy if infile is the same as outfile
@@ -3036,7 +3046,7 @@ meta = [
   "resources_dir": moduleDir.toRealPath().normalize(),
   "config": processConfig(readJsonBlob('''{
   "name" : "concat_text",
-  "version" : "v0.3.1",
+  "version" : "v0.3.2",
   "authors" : [
     {
       "name" : "Toni Verbeiren",
@@ -3265,7 +3275,7 @@ meta = [
       "id" : "docker",
       "image" : "alpine:latest",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.3.1",
+      "target_tag" : "v0.3.2",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3288,23 +3298,23 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/concat_text",
-    "viash_version" : "0.9.4",
+    "viash_version" : "0.9.7",
-    "git_commit" : "4acf73e0255554766186f4016986782c0d25c309",
+    "git_commit" : "7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9",
     "git_remote" : "https://github.com/viash-hub/craftbox"
   },
   "package_config" : {
     "name" : "craftbox",
-    "version" : "v0.3.1",
+    "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 := 'v0.3.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
     ],
     "keywords" : [
       "scripts",
@@ -3798,7 +3808,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/craftbox/concat_text",
-    "tag" : "v0.3.1"
+    "tag" : "v0.3.2"
   },
   "tag" : "$id"
 }'''),

target/nextflow/concat_text/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'concat_text'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.3.1'
+  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, Robrecht Cannoodt'
 }

target/nextflow/csv2fasta/.config.vsh.yaml

@@ -1,5 +1,5 @@
 name: "csv2fasta"
-version: "v0.3.1"
+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: "v0.3.1"
+  target_tag: "v0.3.2"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -256,12 +256,12 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/csv2fasta"
   executable: "target/nextflow/csv2fasta/main.nf"
-  viash_version: "0.9.4"
+  viash_version: "0.9.7"
-  git_commit: "4acf73e0255554766186f4016986782c0d25c309"
+  git_commit: "7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9"
   git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
   name: "craftbox"
-  version: "v0.3.1"
+  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\
@@ -277,14 +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 := 'v0.3.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
   keywords:
   - "scripts"
   - "custom"

target/nextflow/csv2fasta/main.nf

@@ -1,6 +1,6 @@
-// csv2fasta v0.3.1
+// 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
+    while (header == null && (line = br.readLine()) != null) {
-  def header = null
+      if (!line.startsWith("#")) {
-  while (br.ready() && header == null) {
+        header = splitRegex.split(line, -1).collect { field ->
-    def line = br.readLine()
+          def m = removeQuote.matcher(field)
-    row++
+          m.find() ? m.replaceFirst('$1') : field
-    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
         }
       }
-      assert header.size() == data.size(): "Row $row should contain the same number as fields as the header"
+      row++
-      
+    }
-      def dataMap = [header, data].transpose().collectEntries().findAll{it.value != null}
+    assert header != null : "CSV file should contain a header"
-      output.add(dataMap)
+
+    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 '${outfile.toString()}')\"",
+          "[ -d \"\$(dirname '${outfileNoTrailingSlash}')\" ] || mkdir -p \"\$(dirname '${outfileNoTrailingSlash}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+          "cp -a '${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" : "v0.3.1",
+  "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" : "v0.3.1",
+      "target_tag" : "v0.3.2",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3351,23 +3361,23 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/csv2fasta",
-    "viash_version" : "0.9.4",
+    "viash_version" : "0.9.7",
-    "git_commit" : "4acf73e0255554766186f4016986782c0d25c309",
+    "git_commit" : "7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9",
     "git_remote" : "https://github.com/viash-hub/craftbox"
   },
   "package_config" : {
     "name" : "craftbox",
-    "version" : "v0.3.1",
+    "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 := 'v0.3.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
     ],
     "keywords" : [
       "scripts",
@@ -3911,7 +3921,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/craftbox/csv2fasta",
-    "tag" : "v0.3.1"
+    "tag" : "v0.3.2"
   },
   "tag" : "$id"
 }'''),

target/nextflow/csv2fasta/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'csv2fasta'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.3.1'
+  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'
 }

target/nextflow/move_files_to_directory/.config.vsh.yaml

@@ -1,5 +1,5 @@
 name: "move_files_to_directory"
-version: "v0.3.1"
+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:
+    description: "When set, symbolic links are preserved as symbolic links in the\
-    - "-d"
+      \ output directory. By default, symbolic links are dereferenced and the target\
-    description: "Preserve symbolic links."
+      \ 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"
+summary: "Publish one or multiple files or directories to the same output directory."
-description: "This component copies one or multiple files to the same destination\
+description: "This component copies one or multiple files or directories\nto the same\
-  \ directory, creating the output directory if it doesn't exist."
+  \ 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: "v0.3.1"
+  target_tag: "v0.3.2"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -146,18 +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"
+  viash_version: "0.9.7"
-  git_commit: "4acf73e0255554766186f4016986782c0d25c309"
+  git_commit: "7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9"
   git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
   name: "craftbox"
-  version: "v0.3.1"
+  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\
@@ -173,14 +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 := 'v0.3.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
   keywords:
   - "scripts"
   - "custom"

target/nextflow/move_files_to_directory/main.nf

@@ -1,6 +1,6 @@
-// move_files_to_directory v0.3.1
+// 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
+    while (header == null && (line = br.readLine()) != null) {
-  def header = null
+      if (!line.startsWith("#")) {
-  while (br.ready() && header == null) {
+        header = splitRegex.split(line, -1).collect { field ->
-    def line = br.readLine()
+          def m = removeQuote.matcher(field)
-    row++
+          m.find() ? m.replaceFirst('$1') : field
-    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
         }
       }
-      assert header.size() == data.size(): "Row $row should contain the same number as fields as the header"
+      row++
-      
+    }
-      def dataMap = [header, data].transpose().collectEntries().findAll{it.value != null}
+    assert header != null : "CSV file should contain a header"
-      output.add(dataMap)
+
+    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 '${outfile.toString()}')\"",
+          "[ -d \"\$(dirname '${outfileNoTrailingSlash}')\" ] || mkdir -p \"\$(dirname '${outfileNoTrailingSlash}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+          "cp -a '${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" : "v0.3.1",
+  "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" : [
+          "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.",
-            "-d"
-          ],
-          "description" : "Preserve symbolic links.",
           "direction" : "input"
         }
       ]
@@ -3102,8 +3119,8 @@ meta = [
       "is_executable" : true
     }
   ],
-  "summary" : "Publish one or multiple files to the same directory",
+  "summary" : "Publish one or multiple files or directories to the same output 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",
   "test_resources" : [
     {
       "type" : "bash_script",
@@ -3205,7 +3222,7 @@ meta = [
       "id" : "docker",
       "image" : "debian:latest",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.3.1",
+      "target_tag" : "v0.3.2",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3217,6 +3234,10 @@ meta = [
         }
       ]
     },
+    {
+      "type" : "native",
+      "id" : "native"
+    },
     {
       "type" : "native",
       "id" : "native"
@@ -3225,25 +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",
+    "viash_version" : "0.9.7",
-    "git_commit" : "4acf73e0255554766186f4016986782c0d25c309",
+    "git_commit" : "7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9",
     "git_remote" : "https://github.com/viash-hub/craftbox"
   },
   "package_config" : {
     "name" : "craftbox",
-    "version" : "v0.3.1",
+    "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 := 'v0.3.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
     ],
     "keywords" : [
       "scripts",
@@ -3300,27 +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=( )
+# Set copy flags based on options
-
+if [[ "\\$par_keep_symbolic_links" == "true" ]]; then
-if [ "\\$par_keep_symbolic_links" == "true" ]; then
+  # -a implies -dR --preserve=all
-  extra_params+=( "-d" )
+  # 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
+# Process multiple input paths (files or directories)
-IFS=";" read -ra input_files <<< "\\$par_input"
+IFS=";" read -ra input_paths <<< "\\$par_input"
-for file in "\\${input_files[@]}"; do
+for path in "\\${input_paths[@]}"; do
-  # Check if the file exists before copying
+  if [[ -e "\\$path" ]] || [[ -L "\\$path" ]]; then
-  if [[ -f "\\$file" ]]; then
+    cp \\$cp_flags "\\$path" "\\$par_output/"
-
+    echo "Copied \\$path to \\$par_output/"
-    cp \\${extra_params[@]} "\\$file" "\\$par_output/"
-    echo "Copied \\$file 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
@@ -3705,7 +3732,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/craftbox/move_files_to_directory",
-    "tag" : "v0.3.1"
+    "tag" : "v0.3.2"
   },
   "tag" : "$id"
 }'''),

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 = 'v0.3.1'
+  version = 'v0.3.2'
-  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'
   author = 'Dorien Roosen'
 }
 

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": {
+    "inputs": {
-      "title": "Arguments",
+      "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"

target/nextflow/sync_resources/.config.vsh.yaml

@@ -1,5 +1,5 @@
 name: "sync_resources"
-version: "v0.3.1"
+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: "v0.3.1"
+  target_tag: "v0.3.2"
   namespace_separator: "/"
   setup:
   - type: "apk"
@@ -196,12 +196,12 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/sync_resources"
   executable: "target/nextflow/sync_resources/main.nf"
-  viash_version: "0.9.4"
+  viash_version: "0.9.7"
-  git_commit: "4acf73e0255554766186f4016986782c0d25c309"
+  git_commit: "7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9"
   git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
   name: "craftbox"
-  version: "v0.3.1"
+  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\
@@ -217,14 +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 := 'v0.3.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
   keywords:
   - "scripts"
   - "custom"

target/nextflow/sync_resources/main.nf

@@ -1,6 +1,6 @@
-// sync_resources v0.3.1
+// 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
+    while (header == null && (line = br.readLine()) != null) {
-  def header = null
+      if (!line.startsWith("#")) {
-  while (br.ready() && header == null) {
+        header = splitRegex.split(line, -1).collect { field ->
-    def line = br.readLine()
+          def m = removeQuote.matcher(field)
-    row++
+          m.find() ? m.replaceFirst('$1') : field
-    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
         }
       }
-      assert header.size() == data.size(): "Row $row should contain the same number as fields as the header"
+      row++
-      
+    }
-      def dataMap = [header, data].transpose().collectEntries().findAll{it.value != null}
+    assert header != null : "CSV file should contain a header"
-      output.add(dataMap)
+
+    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 '${outfile.toString()}')\"",
+          "[ -d \"\$(dirname '${outfileNoTrailingSlash}')\" ] || mkdir -p \"\$(dirname '${outfileNoTrailingSlash}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+          "cp -a '${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" : "v0.3.1",
+  "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" : "v0.3.1",
+      "target_tag" : "v0.3.2",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3293,23 +3303,23 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/sync_resources",
-    "viash_version" : "0.9.4",
+    "viash_version" : "0.9.7",
-    "git_commit" : "4acf73e0255554766186f4016986782c0d25c309",
+    "git_commit" : "7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9",
     "git_remote" : "https://github.com/viash-hub/craftbox"
   },
   "package_config" : {
     "name" : "craftbox",
-    "version" : "v0.3.1",
+    "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 := 'v0.3.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
     ],
     "keywords" : [
       "scripts",
@@ -3772,7 +3782,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/craftbox/sync_resources",
-    "tag" : "v0.3.1"
+    "tag" : "v0.3.2"
   },
   "tag" : "$id"
 }'''),

target/nextflow/sync_resources/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'sync_resources'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.3.1'
+  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'
 }

target/nextflow/untar/.config.vsh.yaml

@@ -1,5 +1,5 @@
 name: "untar"
-version: "v0.3.1"
+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: "v0.3.1"
+  target_tag: "v0.3.2"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -181,12 +181,12 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/untar"
   executable: "target/nextflow/untar/main.nf"
-  viash_version: "0.9.4"
+  viash_version: "0.9.7"
-  git_commit: "4acf73e0255554766186f4016986782c0d25c309"
+  git_commit: "7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9"
   git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
   name: "craftbox"
-  version: "v0.3.1"
+  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\
@@ -202,14 +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 := 'v0.3.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
   keywords:
   - "scripts"
   - "custom"

target/nextflow/untar/main.nf

@@ -1,6 +1,6 @@
-// untar v0.3.1
+// 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
+    while (header == null && (line = br.readLine()) != null) {
-  def header = null
+      if (!line.startsWith("#")) {
-  while (br.ready() && header == null) {
+        header = splitRegex.split(line, -1).collect { field ->
-    def line = br.readLine()
+          def m = removeQuote.matcher(field)
-    row++
+          m.find() ? m.replaceFirst('$1') : field
-    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
         }
       }
-      assert header.size() == data.size(): "Row $row should contain the same number as fields as the header"
+      row++
-      
+    }
-      def dataMap = [header, data].transpose().collectEntries().findAll{it.value != null}
+    assert header != null : "CSV file should contain a header"
-      output.add(dataMap)
+
+    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 '${outfile.toString()}')\"",
+          "[ -d \"\$(dirname '${outfileNoTrailingSlash}')\" ] || mkdir -p \"\$(dirname '${outfileNoTrailingSlash}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+          "cp -a '${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" : "v0.3.1",
+  "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" : "v0.3.1",
+      "target_tag" : "v0.3.2",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3272,23 +3282,23 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/untar",
-    "viash_version" : "0.9.4",
+    "viash_version" : "0.9.7",
-    "git_commit" : "4acf73e0255554766186f4016986782c0d25c309",
+    "git_commit" : "7d520dc76cb6b3f1eaece9afcc9a3458ca82afe9",
     "git_remote" : "https://github.com/viash-hub/craftbox"
   },
   "package_config" : {
     "name" : "craftbox",
-    "version" : "v0.3.1",
+    "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 := 'v0.3.1'"
+      ".engines[.type == 'docker'].target_tag := 'v0.3.2'"
     ],
     "keywords" : [
       "scripts",
@@ -3762,7 +3772,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/craftbox/untar",
-    "tag" : "v0.3.1"
+    "tag" : "v0.3.2"
   },
   "tag" : "$id"
 }'''),

target/nextflow/untar/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'untar'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.3.1'
+  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'
 }