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)
2026-06-01 12:59:55 +00:00
parent d23cce7a1f
commit f00709ee19
38 changed files with 943 additions and 587 deletions
--- a/target/executable/concat_text/.config.vsh.yaml
+++ b/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\
-    \ of zipped and plain input files\n  2. Allow to specify a compression algorithm\
-    \ for the output\n"
+  improvements: "This component could be improved:\n  1. Allow to specify a compression\
+    \ algorithm for the output\n"
 status: "enabled"
 scope:
  image: "public"
@@ -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"
-  git_commit: "32cec141fe0eb61ce1b63f36a2e5c3ae2fbf9550"
+  viash_version: "0.9.7"
+  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:
--- a/target/executable/concat_text/concat_text
+++ b/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
-
-TMPDIR=\$(mktemp -d "\$meta_temp_dir/concat_text-XXXXXX")
-function clean_up {
-  [[ -d "\$TMPDIR" ]] && rm -r "\$TMPDIR"
+# --- Function to check for GZIP format using the 'file' command ---
+is_gzipped() {
+    # Ensure the file exists and is not empty before checking
+    if [ ! -s "\$1" ]; then
+        return 1
+    fi
+    # Get the MIME type of the file. The '-b' option omits the filename from the output.
+    local mime_type
+    mime_type=\$(file -b --mime-type "\$1")
+    
+    # Check if the MIME type corresponds to gzip.
+    # application/gzip is standard, while application/x-gzip is also commonly seen.
+    if [[ "\$mime_type" == "application/gzip" || "\$mime_type" == "application/x-gzip" ]]; then
+        return 0 # 0 indicates success (true in bash)
+    else
+        return 1 # 1 indicates failure (false in bash)
+    fi
 }
-trap clean_up EXIT

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

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

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

-if [ "\$par_gzip_output" == true ]; then
-  echo ">> Zip output file"
-  gzip \$TMPDIR/contents
-  mv \$TMPDIR/contents.gz \$par_output
-else
-  mv \$TMPDIR/contents \$par_output
-fi
+echo "Script finished successfully."
 VIASHMAIN
 bash "\$tempscript" &
 wait "\$!"