Build branch craftbox/main with version main to craftbox on branch main (b74f552)

Build pipeline: vsh-ci-build-template-xfb9n

Source commit: b74f55253e

Source message: Prepare for 0.3.2 release (#19)

CHANGELOG.md

@@ -1,3 +1,21 @@
+# craftbox 0.3.2
+
+## NEW FEATURES
+
+* `move_files_to_directory`: add support for moving directories (PR #17).
+
+## MINOR CHANGES
+
+* Bump viash to 0.9.7 (PR #18).
+
+# craftbox 0.3.1
+
+## MINOR CHANGES
+
+* `concat_text`: Allow input files to be a mixed bag of gzipped and plain text files (PR #12).
+
+* `concat_text`: Stream concatenated files to gzip (PR #12).
+
 # craftbox 0.3.0
 
 ## NEW FEATURES

README.md

@@ -43,7 +43,7 @@ Viash components in craftbox can be run in various ways:
 
 ``` mermaid lang="mermaid
 flowchart TD
-    A[craftbox v0.3.0] --> B(Viash Hub Launch)
+    A[craftbox v0.3.2] --> B(Viash Hub Launch)
     A --> C(Viash CLI)
     A --> D(Nextflow CLI)
     A --> E(Seqera Cloud)
@@ -53,7 +53,7 @@ flowchart TD
 ### 1. Via the Viash Hub Launch interface
 
 You can run this component directly from the Viash Hub [Launch
-interface](https://www.viash-hub.com/launch?package=craftbox&version=v0.3.0&component=concat_rtext&runner=Executable).
+interface](https://www.viash-hub.com/launch?package=craftbox&version=v0.3.2&component=concat_rtext&runner=Executable).
 
 ![](docs/viash-hub.png)
 
@@ -63,9 +63,9 @@ You can run this component directly from the command line using the
 Viash CLI.
 
 ``` bash
-viash run vsh://craftbox@v0.3.0/concat_rtext -- --help
+viash run vsh://craftbox@v0.3.2/concat_rtext -- --help
 
-viash run vsh://craftbox@v0.3.0/concat_rtext -- \
+viash run vsh://craftbox@v0.3.2/concat_rtext -- \
   --input path/to/input.txt \
   --input path/to/compressed.txt.gz \
   --output path/to/output.txt
@@ -80,7 +80,7 @@ You can run this component as a Nextflow pipeline.
 
 ``` bash
 nextflow run https://packages.viash-hub.com/vsh/craftbox \
-  -revision v0.3.0 \
+  -revision v0.3.2 \
   -main-script target/nextflow/concat_rtext/main.nf \
   -latest -resume \
   -profile docker \
@@ -109,7 +109,7 @@ component as a dependency:
 ``` yaml
 dependencies:
   - name: concat_rtext
-    repository: vsh://craftbox@v0.3.0
+    repository: vsh://craftbox@v0.3.2
 ```
 
 **Tip:** See the [Viash

README.qmd

@@ -7,7 +7,7 @@ license <- paste0(package$links$repository, "/blob/main/LICENSE")
 contributing <- paste0(package$links$repository, "/blob/main/CONTRIBUTING.md")
 
 pkg <- package$name
-ver <- if (!is.null(package$version)) package$version else "v0.3.0"
+ver <- if (!is.null(package$version)) package$version else "v0.3.2"
 comp <- "concat_rtext"
 ```
 # 🪡📦 `r pkg`

_viash.yaml

@@ -18,7 +18,7 @@ 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']
 version: main

src/concat_text/config.vsh.yaml

@@ -1,5 +1,5 @@
 name: concat_text
-summary: Concatenate a number of text files
+summary: Concatenate multiple (possibly gzipped) text files
 description: |
   Concatenate a number of text files, handle gzipped text files gracefully and
   optionally gzip the output text file.
@@ -11,12 +11,13 @@ authors:
     roles: [ author, maintainer ]
   - __merge__: /src/_authors/dries_schaumont.yaml
     roles: [ reviewer ]
+  - __merge__: /src/_authors/robrecht_cannoodt.yaml
+    roles: [ contributor ]
 
 info:
   improvements: |
-    This component could be improved in 2 ways:
+    This component could be improved:
-      1. Allow for a mix of zipped and plain input files
+      1. Allow to specify a compression algorithm for the output
-      2. Allow to specify a compression algorithm for the output
 
 argument_groups:
   - name: Input arguments
@@ -26,14 +27,14 @@ argument_groups:
         type: file
         multiple: true
         required: true
-        example: input?.txt.gz
+        example: input.txt.gz
   - name: Output arguments
     arguments:
       - name: "--gzip_output"
         type: boolean_true
         description: Should the output be zipped?
       - name: --output
-        description: File to write the output to, optionally gzipped.
+        description: File to write the output to, potentially gzipped.
         type: file
         direction: output
         example: output.txt

src/concat_text/script.sh

@@ -1,34 +1,65 @@
 #!/usr/bin/env bash
 
-set -euo pipefail
+set -eo pipefail
 
-TMPDIR=$(mktemp -d "$meta_temp_dir/concat_text-XXXXXX")
+## VIASH START
-function clean_up {
+par_input="README.md;README.qmd"
-  [[ -d "$TMPDIR" ]] && rm -r "$TMPDIR"
+par_output="concatenated_output.txt"
+par_compress_output="true"
+## VIASH END
+
+# --- Function to check for GZIP format using the 'file' command ---
+is_gzipped() {
+    # Ensure the file exists and is not empty before checking
+    if [ ! -s "$1" ]; then
+        return 1
+    fi
+    # Get the MIME type of the file. The '-b' option omits the filename from the output.
+    local mime_type
+    mime_type=$(file -b --mime-type "$1")
+    
+    # Check if the MIME type corresponds to gzip.
+    # application/gzip is standard, while application/x-gzip is also commonly seen.
+    if [[ "$mime_type" == "application/gzip" || "$mime_type" == "application/x-gzip" ]]; then
+        return 0 # 0 indicates success (true in bash)
+    else
+        return 1 # 1 indicates failure (false in bash)
+    fi
 }
-trap clean_up EXIT
 
-par_input="$(echo "$par_input" | tr ';' ' ')"
+# Read the ;-separated file paths from the input variable into an array
+IFS=";" read -ra input_files <<< "$par_input"
 
-echo -n ">> Check if input is gzipped... "
+# Process the files if the array contains any paths
-set +eo pipefail
+if [ ${#input_files[@]} -gt 0 ] && [ -n "${input_files[0]}" ]; then
-file $par_input | grep -q 'gzip'
-is_zipped="$?"
-set -euo pipefail
-[[ "$is_zipped" == "0" ]] && echo "yes" || echo "no"
 
-if [[ "$is_zipped" == "0" ]]; then
+    # Ensure the output file is empty before we start
-  echo ">> zcat gzipped files"
+    > "$par_output"
-  zcat $par_input > $TMPDIR/contents
+
+    echo "Processing files for -> $par_output"
+
+    # Create a subshell for the loop to group all cat/zcat output.
+    (
+        for file in "${input_files[@]}"; do
+            if [ -z "$file" ]; then continue; fi # Skip empty entries in the array
+
+            if is_gzipped "$file"; then
+                zcat "$file"
+            else
+                cat "$file"
+            fi
+        done
+    ) | if [ "$par_compress_output" = "true" ]; then
+        # If compression is enabled, pipe the entire stream to gzip
+        gzip -c >> "$par_output"
+    else
+        # Otherwise, just redirect the stream to the plain text file
+        cat >> "$par_output"
+    fi
+
+    echo "Finished creating $par_output."
 else
-  echo ">> cat plain files"
+    echo "No input files provided in \$par_input. Exiting."
-  cat $par_input > $TMPDIR/contents
 fi
 
-if [ "$par_gzip_output" == true ]; then
+echo "Script finished successfully."
-  echo ">> Zip output file"
-  gzip $TMPDIR/contents
-  mv $TMPDIR/contents.gz $par_output
-else
-  mv $TMPDIR/contents $par_output
-fi

src/concat_text/test.sh

@@ -2,6 +2,65 @@
 
 set -euo pipefail
 
+echo ">> Running concat_text.sh script"
+
+is_gzipped() {
+    # Ensure the file exists and is not empty
+    if [ ! -s "$1" ]; then
+        return 1
+    fi
+    # Get the MIME type of the file
+    local mime_type
+    mime_type=$(file -b --mime-type "$1")
+    
+    # Check if the MIME type corresponds to gzip.
+    if [[ "$mime_type" == "application/gzip" || "$mime_type" == "application/x-gzip" ]]; then
+        return 0
+    else
+        return 1
+    fi
+}
+
+compare_files() {
+  local file1="$1"
+  local file2="$2"
+  if [[ ! -f "$file1" || ! -f "$file2" ]]; then
+    echo "One of the files does not exist: $file1 or $file2"
+    return 1
+  fi
+  # decompress file 1 if need be
+  if is_gzipped "$file1"; then
+    file1=$(mktemp)
+    zcat "$1" > "$file1"
+  fi
+  # decompress file 2 if need be
+  if is_gzipped "$file2"; then
+    file2=$(mktemp)
+    zcat "$2" > "$file2"
+  fi
+
+  if cmp -s "$file1" "$file2"; then
+    echo "Files are identical."
+    return 0
+  else
+    echo "Files differ."
+    echo "Found:"
+    if is_gzipped "$file1"; then
+      zcat "$file1" | od -c
+    else
+      cat "$file1" | od -c
+    fi
+    echo "Expected:"
+    if is_gzipped "$file2"; then
+      zcat "$file2" | od -c
+    else
+      cat "$file2" | od -c
+    fi
+    return 1
+  fi
+}
+
+## TEST RESOURCES
 echo ">> Creating test input files file[1-3].txt"
 INPUT_FILE_1="file1.txt"
 INPUT_FILE_2="file2.txt"
@@ -25,46 +84,31 @@ EOF
 
 gzip -k "expected_output.txt"
 
+## RUN TESTS
 echo ">> Run component on 3 plain input files, plain output"
 $meta_executable \
   --input "$INPUT_FILE_1;$INPUT_FILE_2;$INPUT_FILE_3" \
   --output "output1.txt"
+compare_files "output1.txt" "expected_output.txt"
 
-[[ ! -f "output1.txt" ]] \
+echo ">> Run component on mixed input files, plain output"
-  && echo "Output file output1.txt not found!" && exit 1
-[[ $(cmp "output1.txt" "expected_output.txt") ]] \
-  && echo "Output file output1.txt is not as expected!" && exit 1
-
-echo ">> Run component on 3 zipped input files, plain output"
 $meta_executable \
-  --input "$INPUT_FILE_1.gz;$INPUT_FILE_2.gz;$INPUT_FILE_3.gz" \
+  --input "$INPUT_FILE_1.gz;$INPUT_FILE_2;$INPUT_FILE_3.gz" \
   --output "output2.txt"
-
+compare_files "output2.txt" "expected_output.txt"
-[[ ! -f "output2.txt" ]] \
-  && echo "Output file output2.txt not found!" && exit 1
-[[ $(cmp "output2.txt" "expected_output.txt") ]] \
-  && echo "Output file output2.txt is not as expected!" && exit 1
 
 echo ">> Run component on 3 plain input files, zipped output"
 $meta_executable \
   --input "$INPUT_FILE_1;$INPUT_FILE_2;$INPUT_FILE_3" \
   --output "output3.txt.gz" \
   --gzip_output
+compare_files "output3.txt.gz" "expected_output.txt.gz"
 
-[[ ! -f "output3.txt.gz" ]] \
+echo ">> Run component on mixed input files, zipped output"
-  && echo "Output file output3.txt.gz not found!" && exit 1
-[[ $(cmp "output3.txt.gz" "expected_output.txt.gz") ]] \
-  && echo "Output file output3.txt.gz is not as expected!" && exit 1
-
-echo ">> Run component on 3 zipped input files, zipped output"
 $meta_executable \
-  --input "$INPUT_FILE_1.gz;$INPUT_FILE_2.gz;$INPUT_FILE_3.gz" \
+  --input "$INPUT_FILE_1.gz;$INPUT_FILE_2;$INPUT_FILE_3.gz" \
   --output "output4.txt.gz" \
   --gzip_output
-
+compare_files "output4.txt.gz" "expected_output.txt.gz"
-[[ ! -f "output4.txt.gz" ]] \
-  && echo "Output file output4.txt.gz not found!" && exit 1
-[[ $(cmp "output4.txt.gz" "expected_output.txt.gz") ]] \
-  && echo "Output file output4.txt.gz is not as expected!" && exit 1
 
 echo ">> Tests done"

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

@@ -156,8 +156,8 @@ 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: "32cec141fe0eb61ce1b63f36a2e5c3ae2fbf9550"
+  git_commit: "b74f55253eaa60d4dcd40a80b6965bc0bc9e1dd1"
   git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
   name: "craftbox"
@@ -177,7 +177,7 @@ 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:

target/executable/check_disk_space/check_disk_space

@@ -2,7 +2,7 @@
 
 # check_disk_space main
 # 
-# 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.
 # 
@@ -446,9 +446,9 @@ function ViashDockerfile {
 FROM bash:latest
 ENTRYPOINT []
 LABEL org.opencontainers.image.description="Companion container for running component check_disk_space"
-LABEL org.opencontainers.image.created="2025-09-01T14:32:38Z"
+LABEL org.opencontainers.image.created="2026-06-01T12:52:41Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/craftbox"
-LABEL org.opencontainers.image.revision="32cec141fe0eb61ce1b63f36a2e5c3ae2fbf9550"
+LABEL org.opencontainers.image.revision="b74f55253eaa60d4dcd40a80b6965bc0bc9e1dd1"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -26,6 +26,22 @@ authors:
     - name: "Data Intuitive"
       href: "https://www.data-intuitive.com"
       role: "Data Scientist"
+- name: "Robrecht Cannoodt"
+  roles:
+  - "contributor"
+  info:
+    links:
+      email: "robrecht@data-intuitive.com"
+      github: "rcannood"
+      orcid: "0000-0003-3641-729X"
+      linkedin: "robrechtcannoodt"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Science Engineer"
+    - name: "Open Problems"
+      href: "https://openproblems.bio"
+      role: "Core Member"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -34,7 +50,7 @@ argument_groups:
     description: "A list of (gzipped) text files."
     info: null
     example:
-    - "input?.txt.gz"
+    - "input.txt.gz"
     must_exist: true
     create_parent: true
     required: true
@@ -50,7 +66,7 @@ argument_groups:
     direction: "input"
   - type: "file"
     name: "--output"
-    description: "File to write the output to, optionally gzipped."
+    description: "File to write the output to, potentially gzipped."
     info: null
     example:
     - "output.txt"
@@ -64,7 +80,7 @@ resources:
 - type: "bash_script"
   path: "script.sh"
   is_executable: true
-summary: "Concatenate a number of text files"
+summary: "Concatenate multiple (possibly gzipped) text files"
 description: "Concatenate a number of text files, handle gzipped text files gracefully\
   \ and\noptionally gzip the output text file.\n\nThis component is useful for concatening\
   \ fastq files from different lanes, for instance.\n"
@@ -73,9 +89,8 @@ test_resources:
   path: "test.sh"
   is_executable: true
 info:
-  improvements: "This component could be improved in 2 ways:\n  1. Allow for a mix\
+  improvements: "This component could be improved:\n  1. Allow to specify a compression\
-    \ of zipped and plain input files\n  2. Allow to specify a compression algorithm\
+    \ algorithm for the output\n"
-    \ for the output\n"
 status: "enabled"
 scope:
   image: "public"
@@ -174,8 +189,8 @@ 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: "32cec141fe0eb61ce1b63f36a2e5c3ae2fbf9550"
+  git_commit: "b74f55253eaa60d4dcd40a80b6965bc0bc9e1dd1"
   git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
   name: "craftbox"
@@ -195,7 +210,7 @@ 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:

target/executable/concat_text/concat_text

@@ -2,7 +2,7 @@
 
 # concat_text main
 # 
-# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.7 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -14,6 +14,7 @@
 # Component authors:
 #  * Toni Verbeiren (author, maintainer)
 #  * Dries Schaumont (reviewer)
+#  * Robrecht Cannoodt (contributor)
 
 set -e
 
@@ -451,11 +452,11 @@ FROM alpine:latest
 ENTRYPOINT []
 RUN apk add --no-cache bash procps file
 
-LABEL org.opencontainers.image.authors="Toni Verbeiren, Dries Schaumont"
+LABEL org.opencontainers.image.authors="Toni Verbeiren, Dries Schaumont, Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component concat_text"
-LABEL org.opencontainers.image.created="2025-09-01T14:32:38Z"
+LABEL org.opencontainers.image.created="2026-06-01T12:52:41Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/craftbox"
-LABEL org.opencontainers.image.revision="32cec141fe0eb61ce1b63f36a2e5c3ae2fbf9550"
+LABEL org.opencontainers.image.revision="b74f55253eaa60d4dcd40a80b6965bc0bc9e1dd1"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -584,7 +585,7 @@ function ViashHelp {
   echo "Input arguments:"
   echo "    --input"
   echo "        type: file, required parameter, multiple values allowed, file must exist"
-  echo "        example: input?.txt.gz"
+  echo "        example: input.txt.gz"
   echo "        A list of (gzipped) text files."
   echo ""
   echo "Output arguments:"
@@ -595,7 +596,7 @@ function ViashHelp {
   echo "    --output"
   echo "        type: file, output, file must exist"
   echo "        example: output.txt"
-  echo "        File to write the output to, optionally gzipped."
+  echo "        File to write the output to, potentially gzipped."
   echo ""
   echo "Viash built in Computational Requirements:"
   echo "    ---cpus=INT"
@@ -1080,6 +1081,10 @@ function interrupt {
 trap clean_up EXIT
 trap interrupt INT SIGINT
 cat > "\$tempscript" << 'VIASHMAIN'
+#!/usr/bin/env bash
+
+set -eo pipefail
+
 ## VIASH START
 # The following code has been auto-generated by Viash.
 $( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "${VIASH_PAR_INPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_input='&'#" ; else echo "# par_input="; fi )
@@ -1105,40 +1110,62 @@ $( if [ ! -z ${VIASH_META_MEMORY_TIB+x} ]; then echo "${VIASH_META_MEMORY_TIB}"
 $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_pib='&'#" ; else echo "# meta_memory_pib="; fi )
 
 ## VIASH END
-#!/usr/bin/env bash
 
-set -euo pipefail
+# --- Function to check for GZIP format using the 'file' command ---
-
+is_gzipped() {
-TMPDIR=\$(mktemp -d "\$meta_temp_dir/concat_text-XXXXXX")
+    # Ensure the file exists and is not empty before checking
-function clean_up {
+    if [ ! -s "\$1" ]; then
-  [[ -d "\$TMPDIR" ]] && rm -r "\$TMPDIR"
+        return 1
+    fi
+    # Get the MIME type of the file. The '-b' option omits the filename from the output.
+    local mime_type
+    mime_type=\$(file -b --mime-type "\$1")
+    
+    # Check if the MIME type corresponds to gzip.
+    # application/gzip is standard, while application/x-gzip is also commonly seen.
+    if [[ "\$mime_type" == "application/gzip" || "\$mime_type" == "application/x-gzip" ]]; then
+        return 0 # 0 indicates success (true in bash)
+    else
+        return 1 # 1 indicates failure (false in bash)
+    fi
 }
-trap clean_up EXIT
 
-par_input="\$(echo "\$par_input" | tr ';' ' ')"
+# Read the ;-separated file paths from the input variable into an array
+IFS=";" read -ra input_files <<< "\$par_input"
 
-echo -n ">> Check if input is gzipped... "
+# Process the files if the array contains any paths
-set +eo pipefail
+if [ \${#input_files[@]} -gt 0 ] && [ -n "\${input_files[0]}" ]; then
-file \$par_input | grep -q 'gzip'
-is_zipped="\$?"
-set -euo pipefail
-[[ "\$is_zipped" == "0" ]] && echo "yes" || echo "no"
 
-if [[ "\$is_zipped" == "0" ]]; then
+    # Ensure the output file is empty before we start
-  echo ">> zcat gzipped files"
+    > "\$par_output"
-  zcat \$par_input > \$TMPDIR/contents
+
+    echo "Processing files for -> \$par_output"
+
+    # Create a subshell for the loop to group all cat/zcat output.
+    (
+        for file in "\${input_files[@]}"; do
+            if [ -z "\$file" ]; then continue; fi # Skip empty entries in the array
+
+            if is_gzipped "\$file"; then
+                zcat "\$file"
+            else
+                cat "\$file"
+            fi
+        done
+    ) | if [ "\$par_compress_output" = "true" ]; then
+        # If compression is enabled, pipe the entire stream to gzip
+        gzip -c >> "\$par_output"
+    else
+        # Otherwise, just redirect the stream to the plain text file
+        cat >> "\$par_output"
+    fi
+
+    echo "Finished creating \$par_output."
 else
-  echo ">> cat plain files"
+    echo "No input files provided in \\\$par_input. Exiting."
-  cat \$par_input > \$TMPDIR/contents
 fi
 
-if [ "\$par_gzip_output" == true ]; then
+echo "Script finished successfully."
-  echo ">> Zip output file"
-  gzip \$TMPDIR/contents
-  mv \$TMPDIR/contents.gz \$par_output
-else
-  mv \$TMPDIR/contents \$par_output
-fi
 VIASHMAIN
 bash "\$tempscript" &
 wait "\$!"

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

@@ -256,8 +256,8 @@ 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: "32cec141fe0eb61ce1b63f36a2e5c3ae2fbf9550"
+  git_commit: "b74f55253eaa60d4dcd40a80b6965bc0bc9e1dd1"
   git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
   name: "craftbox"
@@ -277,7 +277,7 @@ 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:

target/executable/csv2fasta/csv2fasta

@@ -2,7 +2,7 @@
 
 # csv2fasta main
 # 
-# 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.
 # 
@@ -458,9 +458,9 @@ 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="2025-09-01T14:32:38Z"
+LABEL org.opencontainers.image.created="2026-06-01T12:52:41Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/craftbox"
-LABEL org.opencontainers.image.revision="32cec141fe0eb61ce1b63f36a2e5c3ae2fbf9550"
+LABEL org.opencontainers.image.revision="b74f55253eaa60d4dcd40a80b6965bc0bc9e1dd1"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -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"
@@ -146,14 +151,16 @@ 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: "32cec141fe0eb61ce1b63f36a2e5c3ae2fbf9550"
+  git_commit: "b74f55253eaa60d4dcd40a80b6965bc0bc9e1dd1"
   git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
   name: "craftbox"
@@ -173,7 +180,7 @@ 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:

target/executable/move_files_to_directory/move_files_to_directory

@@ -2,7 +2,7 @@
 
 # move_files_to_directory main
 # 
-# 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.
 # 
@@ -454,9 +454,9 @@ 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="2025-09-01T14:32:38Z"
+LABEL org.opencontainers.image.created="2026-06-01T12:52:41Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/craftbox"
-LABEL org.opencontainers.image.revision="32cec141fe0eb61ce1b63f36a2e5c3ae2fbf9550"
+LABEL org.opencontainers.image.revision="b74f55253eaa60d4dcd40a80b6965bc0bc9e1dd1"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -576,21 +576,27 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 function ViashHelp {
   echo "move_files_to_directory main"
   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"
 }
 
@@ -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
 
@@ -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

@@ -196,8 +196,8 @@ 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: "32cec141fe0eb61ce1b63f36a2e5c3ae2fbf9550"
+  git_commit: "b74f55253eaa60d4dcd40a80b6965bc0bc9e1dd1"
   git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
   name: "craftbox"
@@ -217,7 +217,7 @@ 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:

target/executable/sync_resources/sync_resources

@@ -2,7 +2,7 @@
 
 # sync_resources main
 # 
-# 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.
 # 
@@ -455,9 +455,9 @@ 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="2025-09-01T14:32:37Z"
+LABEL org.opencontainers.image.created="2026-06-01T12:52:41Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/craftbox"
-LABEL org.opencontainers.image.revision="32cec141fe0eb61ce1b63f36a2e5c3ae2fbf9550"
+LABEL org.opencontainers.image.revision="b74f55253eaa60d4dcd40a80b6965bc0bc9e1dd1"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -181,8 +181,8 @@ 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: "32cec141fe0eb61ce1b63f36a2e5c3ae2fbf9550"
+  git_commit: "b74f55253eaa60d4dcd40a80b6965bc0bc9e1dd1"
   git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
   name: "craftbox"
@@ -202,7 +202,7 @@ 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:

target/executable/untar/untar

@@ -2,7 +2,7 @@
 
 # untar main
 # 
-# 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.
 # 
@@ -455,9 +455,9 @@ 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="2025-09-01T14:32:37Z"
+LABEL org.opencontainers.image.created="2026-06-01T12:52:41Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/craftbox"
-LABEL org.opencontainers.image.revision="32cec141fe0eb61ce1b63f36a2e5c3ae2fbf9550"
+LABEL org.opencontainers.image.revision="b74f55253eaa60d4dcd40a80b6965bc0bc9e1dd1"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -156,8 +156,8 @@ 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: "32cec141fe0eb61ce1b63f36a2e5c3ae2fbf9550"
+  git_commit: "b74f55253eaa60d4dcd40a80b6965bc0bc9e1dd1"
   git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
   name: "craftbox"
@@ -177,7 +177,7 @@ 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:

target/nextflow/check_disk_space/main.nf

@@ -1,6 +1,6 @@
 // check_disk_space main
 // 
-// 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
@@ -3215,8 +3225,8 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/check_disk_space",
-    "viash_version" : "0.9.4",
+    "viash_version" : "0.9.7",
-    "git_commit" : "32cec141fe0eb61ce1b63f36a2e5c3ae2fbf9550",
+    "git_commit" : "b74f55253eaa60d4dcd40a80b6965bc0bc9e1dd1",
     "git_remote" : "https://github.com/viash-hub/craftbox"
   },
   "package_config" : {
@@ -3224,7 +3234,7 @@ meta = [
     "version" : "main",
     "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" : [

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

@@ -26,6 +26,22 @@ authors:
     - name: "Data Intuitive"
       href: "https://www.data-intuitive.com"
       role: "Data Scientist"
+- name: "Robrecht Cannoodt"
+  roles:
+  - "contributor"
+  info:
+    links:
+      email: "robrecht@data-intuitive.com"
+      github: "rcannood"
+      orcid: "0000-0003-3641-729X"
+      linkedin: "robrechtcannoodt"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Science Engineer"
+    - name: "Open Problems"
+      href: "https://openproblems.bio"
+      role: "Core Member"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -34,7 +50,7 @@ argument_groups:
     description: "A list of (gzipped) text files."
     info: null
     example:
-    - "input?.txt.gz"
+    - "input.txt.gz"
     must_exist: true
     create_parent: true
     required: true
@@ -50,7 +66,7 @@ argument_groups:
     direction: "input"
   - type: "file"
     name: "--output"
-    description: "File to write the output to, optionally gzipped."
+    description: "File to write the output to, potentially gzipped."
     info: null
     example:
     - "output.txt"
@@ -64,7 +80,7 @@ resources:
 - type: "bash_script"
   path: "script.sh"
   is_executable: true
-summary: "Concatenate a number of text files"
+summary: "Concatenate multiple (possibly gzipped) text files"
 description: "Concatenate a number of text files, handle gzipped text files gracefully\
   \ and\noptionally gzip the output text file.\n\nThis component is useful for concatening\
   \ fastq files from different lanes, for instance.\n"
@@ -73,9 +89,8 @@ test_resources:
   path: "test.sh"
   is_executable: true
 info:
-  improvements: "This component could be improved in 2 ways:\n  1. Allow for a mix\
+  improvements: "This component could be improved:\n  1. Allow to specify a compression\
-    \ of zipped and plain input files\n  2. Allow to specify a compression algorithm\
+    \ algorithm for the output\n"
-    \ for the output\n"
 status: "enabled"
 scope:
   image: "public"
@@ -174,8 +189,8 @@ 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: "32cec141fe0eb61ce1b63f36a2e5c3ae2fbf9550"
+  git_commit: "b74f55253eaa60d4dcd40a80b6965bc0bc9e1dd1"
   git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
   name: "craftbox"
@@ -195,7 +210,7 @@ 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:

target/nextflow/concat_text/main.nf

@@ -1,6 +1,6 @@
 // concat_text main
 // 
-// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.7 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -12,6 +12,7 @@
 // Component authors:
 //  * Toni Verbeiren (author, maintainer)
 //  * Dries Schaumont (reviewer)
+//  * Robrecht Cannoodt (contributor)
 
 ////////////////////////////
 // VDSL3 helper functions //
@@ -1354,47 +1355,42 @@ def readCsv(file_path) {
   def splitRegex = java.util.regex.Pattern.compile(''',(?=(?:[^"]*"[^"]*")*[^"]*$)''')
   def removeQuote = java.util.regex.Pattern.compile('''"(.*)"''')
 
-  def br = java.nio.file.Files.newBufferedReader(inputFile)
+  java.nio.file.Files.newBufferedReader(inputFile).withCloseable { br ->
+    def row = 0
+    def header = null
+    def line
 
-  def row = -1
+    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 +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
@@ -3077,6 +3088,32 @@ meta = [
           }
         ]
       }
+    },
+    {
+      "name" : "Robrecht Cannoodt",
+      "roles" : [
+        "contributor"
+      ],
+      "info" : {
+        "links" : {
+          "email" : "robrecht@data-intuitive.com",
+          "github" : "rcannood",
+          "orcid" : "0000-0003-3641-729X",
+          "linkedin" : "robrechtcannoodt"
+        },
+        "organizations" : [
+          {
+            "name" : "Data Intuitive",
+            "href" : "https://www.data-intuitive.com",
+            "role" : "Data Science Engineer"
+          },
+          {
+            "name" : "Open Problems",
+            "href" : "https://openproblems.bio",
+            "role" : "Core Member"
+          }
+        ]
+      }
     }
   ],
   "argument_groups" : [
@@ -3088,7 +3125,7 @@ meta = [
           "name" : "--input",
           "description" : "A list of (gzipped) text files.",
           "example" : [
-            "input?.txt.gz"
+            "input.txt.gz"
           ],
           "must_exist" : true,
           "create_parent" : true,
@@ -3111,7 +3148,7 @@ meta = [
         {
           "type" : "file",
           "name" : "--output",
-          "description" : "File to write the output to, optionally gzipped.",
+          "description" : "File to write the output to, potentially gzipped.",
           "example" : [
             "output.txt"
           ],
@@ -3132,7 +3169,7 @@ meta = [
       "is_executable" : true
     }
   ],
-  "summary" : "Concatenate a number of text files",
+  "summary" : "Concatenate multiple (possibly gzipped) text files",
   "description" : "Concatenate a number of text files, handle gzipped text files gracefully and\noptionally gzip the output text file.\n\nThis component is useful for concatening fastq files from different lanes, for instance.\n",
   "test_resources" : [
     {
@@ -3142,7 +3179,7 @@ meta = [
     }
   ],
   "info" : {
-    "improvements" : "This component could be improved in 2 ways:\n  1. Allow for a mix of zipped and plain input files\n  2. Allow to specify a compression algorithm for the output\n"
+    "improvements" : "This component could be improved:\n  1. Allow to specify a compression algorithm for the output\n"
   },
   "status" : "enabled",
   "scope" : {
@@ -3261,8 +3298,8 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/concat_text",
-    "viash_version" : "0.9.4",
+    "viash_version" : "0.9.7",
-    "git_commit" : "32cec141fe0eb61ce1b63f36a2e5c3ae2fbf9550",
+    "git_commit" : "b74f55253eaa60d4dcd40a80b6965bc0bc9e1dd1",
     "git_remote" : "https://github.com/viash-hub/craftbox"
   },
   "package_config" : {
@@ -3270,7 +3307,7 @@ meta = [
     "version" : "main",
     "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" : [
@@ -3304,6 +3341,10 @@ def innerWorkflowFactory(args) {
   def rawScript = '''set -e
 tempscript=".viash_script.sh"
 cat > "$tempscript" << VIASHMAIN
+#!/usr/bin/env bash
+
+set -eo pipefail
+
 ## VIASH START
 # The following code has been auto-generated by Viash.
 $( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "${VIASH_PAR_INPUT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_input='&'#" ; else echo "# par_input="; fi )
@@ -3329,40 +3370,62 @@ $( if [ ! -z ${VIASH_META_MEMORY_TIB+x} ]; then echo "${VIASH_META_MEMORY_TIB}"
 $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_memory_pib='&'#" ; else echo "# meta_memory_pib="; fi )
 
 ## VIASH END
-#!/usr/bin/env bash
 
-set -euo pipefail
+# --- Function to check for GZIP format using the 'file' command ---
-
+is_gzipped() {
-TMPDIR=\\$(mktemp -d "\\$meta_temp_dir/concat_text-XXXXXX")
+    # Ensure the file exists and is not empty before checking
-function clean_up {
+    if [ ! -s "\\$1" ]; then
-  [[ -d "\\$TMPDIR" ]] && rm -r "\\$TMPDIR"
+        return 1
+    fi
+    # Get the MIME type of the file. The '-b' option omits the filename from the output.
+    local mime_type
+    mime_type=\\$(file -b --mime-type "\\$1")
+    
+    # Check if the MIME type corresponds to gzip.
+    # application/gzip is standard, while application/x-gzip is also commonly seen.
+    if [[ "\\$mime_type" == "application/gzip" || "\\$mime_type" == "application/x-gzip" ]]; then
+        return 0 # 0 indicates success (true in bash)
+    else
+        return 1 # 1 indicates failure (false in bash)
+    fi
 }
-trap clean_up EXIT
 
-par_input="\\$(echo "\\$par_input" | tr ';' ' ')"
+# Read the ;-separated file paths from the input variable into an array
+IFS=";" read -ra input_files <<< "\\$par_input"
 
-echo -n ">> Check if input is gzipped... "
+# Process the files if the array contains any paths
-set +eo pipefail
+if [ \\${#input_files[@]} -gt 0 ] && [ -n "\\${input_files[0]}" ]; then
-file \\$par_input | grep -q 'gzip'
-is_zipped="\\$?"
-set -euo pipefail
-[[ "\\$is_zipped" == "0" ]] && echo "yes" || echo "no"
 
-if [[ "\\$is_zipped" == "0" ]]; then
+    # Ensure the output file is empty before we start
-  echo ">> zcat gzipped files"
+    > "\\$par_output"
-  zcat \\$par_input > \\$TMPDIR/contents
+
+    echo "Processing files for -> \\$par_output"
+
+    # Create a subshell for the loop to group all cat/zcat output.
+    (
+        for file in "\\${input_files[@]}"; do
+            if [ -z "\\$file" ]; then continue; fi # Skip empty entries in the array
+
+            if is_gzipped "\\$file"; then
+                zcat "\\$file"
+            else
+                cat "\\$file"
+            fi
+        done
+    ) | if [ "\\$par_compress_output" = "true" ]; then
+        # If compression is enabled, pipe the entire stream to gzip
+        gzip -c >> "\\$par_output"
+    else
+        # Otherwise, just redirect the stream to the plain text file
+        cat >> "\\$par_output"
+    fi
+
+    echo "Finished creating \\$par_output."
 else
-  echo ">> cat plain files"
+    echo "No input files provided in \\\\\\$par_input. Exiting."
-  cat \\$par_input > \\$TMPDIR/contents
 fi
 
-if [ "\\$par_gzip_output" == true ]; then
+echo "Script finished successfully."
-  echo ">> Zip output file"
-  gzip \\$TMPDIR/contents
-  mv \\$TMPDIR/contents.gz \\$par_output
-else
-  mv \\$TMPDIR/contents \\$par_output
-fi
 VIASHMAIN
 bash "$tempscript"
 '''

target/nextflow/concat_text/nextflow.config

@@ -4,7 +4,7 @@ manifest {
   nextflowVersion = '!>=20.12.1-edge'
   version = 'main'
   description = 'Concatenate a number of text files, handle gzipped text files gracefully and\noptionally gzip the output text file.\n\nThis component is useful for concatening fastq files from different lanes, for instance.\n'
-  author = 'Toni Verbeiren, Dries Schaumont'
+  author = 'Toni Verbeiren, Dries Schaumont, Robrecht Cannoodt'
 }
 
 process.container = 'nextflow/bash:latest'

target/nextflow/concat_text/nextflow_schema.json

@@ -17,7 +17,7 @@
           "format": "path",
           "exists": true,
           "description": "A list of (gzipped) text files.",
-          "help_text": "Type: `file`, multiple: `True`, required, direction: `input`, example: `[\"input?.txt.gz\"]`. "
+          "help_text": "Type: `file`, multiple: `True`, required, direction: `input`, example: `[\"input.txt.gz\"]`. "
         }
       }
     },
@@ -35,7 +35,7 @@
         "output": {
           "type": "string",
           "format": "path",
-          "description": "File to write the output to, optionally gzipped.",
+          "description": "File to write the output to, potentially gzipped.",
           "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output.txt\"`, direction: `output`, example: `\"output.txt\"`. ",
           "default": "$id.$key.output.txt"
         }

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

@@ -256,8 +256,8 @@ 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: "32cec141fe0eb61ce1b63f36a2e5c3ae2fbf9550"
+  git_commit: "b74f55253eaa60d4dcd40a80b6965bc0bc9e1dd1"
   git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
   name: "craftbox"
@@ -277,7 +277,7 @@ 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:

target/nextflow/csv2fasta/main.nf

@@ -1,6 +1,6 @@
 // csv2fasta main
 // 
-// 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
@@ -3351,8 +3361,8 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/csv2fasta",
-    "viash_version" : "0.9.4",
+    "viash_version" : "0.9.7",
-    "git_commit" : "32cec141fe0eb61ce1b63f36a2e5c3ae2fbf9550",
+    "git_commit" : "b74f55253eaa60d4dcd40a80b6965bc0bc9e1dd1",
     "git_remote" : "https://github.com/viash-hub/craftbox"
   },
   "package_config" : {
@@ -3360,7 +3370,7 @@ meta = [
     "version" : "main",
     "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" : [

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

@@ -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"
@@ -146,14 +151,16 @@ 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: "32cec141fe0eb61ce1b63f36a2e5c3ae2fbf9550"
+  git_commit: "b74f55253eaa60d4dcd40a80b6965bc0bc9e1dd1"
   git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
   name: "craftbox"
@@ -173,7 +180,7 @@ 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:

target/nextflow/move_files_to_directory/main.nf

@@ -1,6 +1,6 @@
 // move_files_to_directory main
 // 
-// 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
@@ -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",
@@ -3217,6 +3234,10 @@ meta = [
         }
       ]
     },
+    {
+      "type" : "native",
+      "id" : "native"
+    },
     {
       "type" : "native",
       "id" : "native"
@@ -3225,10 +3246,10 @@ 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" : "32cec141fe0eb61ce1b63f36a2e5c3ae2fbf9550",
+    "git_commit" : "b74f55253eaa60d4dcd40a80b6965bc0bc9e1dd1",
     "git_remote" : "https://github.com/viash-hub/craftbox"
   },
   "package_config" : {
@@ -3236,7 +3257,7 @@ meta = [
     "version" : "main",
     "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" : [
@@ -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

target/nextflow/move_files_to_directory/nextflow.config

@@ -3,7 +3,7 @@ manifest {
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
   version = 'main'
-  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

@@ -196,8 +196,8 @@ 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: "32cec141fe0eb61ce1b63f36a2e5c3ae2fbf9550"
+  git_commit: "b74f55253eaa60d4dcd40a80b6965bc0bc9e1dd1"
   git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
   name: "craftbox"
@@ -217,7 +217,7 @@ 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:

target/nextflow/sync_resources/main.nf

@@ -1,6 +1,6 @@
 // sync_resources main
 // 
-// 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
@@ -3293,8 +3303,8 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/sync_resources",
-    "viash_version" : "0.9.4",
+    "viash_version" : "0.9.7",
-    "git_commit" : "32cec141fe0eb61ce1b63f36a2e5c3ae2fbf9550",
+    "git_commit" : "b74f55253eaa60d4dcd40a80b6965bc0bc9e1dd1",
     "git_remote" : "https://github.com/viash-hub/craftbox"
   },
   "package_config" : {
@@ -3302,7 +3312,7 @@ meta = [
     "version" : "main",
     "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" : [

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

@@ -181,8 +181,8 @@ 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: "32cec141fe0eb61ce1b63f36a2e5c3ae2fbf9550"
+  git_commit: "b74f55253eaa60d4dcd40a80b6965bc0bc9e1dd1"
   git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
   name: "craftbox"
@@ -202,7 +202,7 @@ 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:

target/nextflow/untar/main.nf

@@ -1,6 +1,6 @@
 // untar main
 // 
-// 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
@@ -3272,8 +3282,8 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/untar",
-    "viash_version" : "0.9.4",
+    "viash_version" : "0.9.7",
-    "git_commit" : "32cec141fe0eb61ce1b63f36a2e5c3ae2fbf9550",
+    "git_commit" : "b74f55253eaa60d4dcd40a80b6965bc0bc9e1dd1",
     "git_remote" : "https://github.com/viash-hub/craftbox"
   },
   "package_config" : {
@@ -3281,7 +3291,7 @@ meta = [
     "version" : "main",
     "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" : [