Build branch main with version main (f91567d)

Build pipeline: viash-hub.biobox.main-cc5jz Source commit: f91567d467 Source message: add outdir argument (#181) * add outdir argument * added tests, small changes * update example outdir
2025-06-24 10:57:17 +00:00
parent 71f1661df8
commit 9cc17eaa6f
341 changed files with 923 additions and 726 deletions
--- a/target/executable/fastqc/.config.vsh.yaml
+++ b/target/executable/fastqc/.config.vsh.yaml
@@ -29,6 +29,18 @@ argument_groups:
  description: "At least one of the output options (--html, --zip, --summary, --data)\
    \ must be used.\n"
  arguments:
+  - type: "file"
+    name: "--outdir"
+    description: "Output directory where the results will be saved.\n"
+    info: null
+    example:
+    - "results"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
  - type: "file"
    name: "--html"
    description: "Create the HTML report of the results. \n'*' wild card must be provided\
@@ -339,9 +351,9 @@ build_info:
  output: "target/executable/fastqc"
  executable: "target/executable/fastqc/fastqc"
  viash_version: "0.9.4"
-  git_commit: "219ba1d3d0d7fbc66393595534bb6c333b08b238"
+  git_commit: "f91567d467e6be79a5f71b24a54864ab13bdd278"
  git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-37-g219ba1d"
+  git_tag: "v0.2.0-38-gf91567d"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/fastqc/fastqc
+++ b/target/executable/fastqc/fastqc
@@ -452,9 +452,9 @@ RUN echo "fastqc: $(fastqc --version | sed -n 's/^FastQC //p')" > /var/software_

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component fastqc"
-LABEL org.opencontainers.image.created="2025-06-23T06:29:32Z"
+LABEL org.opencontainers.image.created="2025-06-24T10:40:49Z"
 LABEL org.opencontainers.image.source="https://github.com/s-andrews/FastQC"
-LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
+LABEL org.opencontainers.image.revision="f91567d467e6be79a5f71b24a54864ab13bdd278"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
@@ -586,6 +586,11 @@ function ViashHelp {
  echo "    At least one of the output options (--html, --zip, --summary, --data) must"
  echo "    be used."
  echo ""
+  echo "    --outdir"
+  echo "        type: file, output, file must exist"
+  echo "        example: results"
+  echo "        Output directory where the results will be saved."
+  echo ""
  echo "    --html"
  echo "        type: file, multiple values allowed, output, file must exist"
  echo "        example: *.html"
@@ -786,6 +791,17 @@ while [[ $# -gt 0 ]]; do
            fi
            shift 1
            ;;
+        --outdir)
+            [ -n "$VIASH_PAR_OUTDIR" ] && ViashError Bad arguments for option \'--outdir\': \'$VIASH_PAR_OUTDIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_OUTDIR="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outdir. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --outdir=*)
+            [ -n "$VIASH_PAR_OUTDIR" ] && ViashError Bad arguments for option \'--outdir=*\': \'$VIASH_PAR_OUTDIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_OUTDIR=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
        --html)
            [ -n "$VIASH_PAR_HTML" ] && ViashError Bad arguments for option \'--html\': \'$VIASH_PAR_HTML\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_HTML="$2"
@@ -1341,6 +1357,9 @@ if [[ -n "$VIASH_META_MEMORY_PIB" ]]; then
 fi

 # create parent directories of output files, if so desired
+if [ ! -z "$VIASH_PAR_OUTDIR" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTDIR")" ]; then
+  mkdir -p "$(dirname "$VIASH_PAR_OUTDIR")"
+fi
 if [ ! -z "$VIASH_PAR_HTML" ] && [ ! -d "$(dirname "$VIASH_PAR_HTML")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_HTML")"
 fi
@@ -1377,6 +1396,11 @@ if [ ! -z "$VIASH_PAR_INPUT" ]; then
  done
  VIASH_PAR_INPUT=$(IFS=';' ; echo "${VIASH_TEST_INPUT[*]}")
 fi
+if [ ! -z "$VIASH_PAR_OUTDIR" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTDIR")" )
+  VIASH_PAR_OUTDIR=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTDIR")
+  VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTDIR" )
+fi
 if [ ! -z "$VIASH_PAR_HTML" ]; then
  VIASH_TEST_HTML=()
  IFS=';'
@@ -1509,6 +1533,7 @@ cat > "\$tempscript" << 'VIASHMAIN'
 ## 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 )
+$( if [ ! -z ${VIASH_PAR_OUTDIR+x} ]; then echo "${VIASH_PAR_OUTDIR}" | sed "s#'#'\"'\"'#g;s#.*#par_outdir='&'#" ; else echo "# par_outdir="; fi )
 $( if [ ! -z ${VIASH_PAR_HTML+x} ]; then echo "${VIASH_PAR_HTML}" | sed "s#'#'\"'\"'#g;s#.*#par_html='&'#" ; else echo "# par_html="; fi )
 $( if [ ! -z ${VIASH_PAR_ZIP+x} ]; then echo "${VIASH_PAR_ZIP}" | sed "s#'#'\"'\"'#g;s#.*#par_zip='&'#" ; else echo "# par_zip="; fi )
 $( if [ ! -z ${VIASH_PAR_SUMMARY+x} ]; then echo "${VIASH_PAR_SUMMARY}" | sed "s#'#'\"'\"'#g;s#.*#par_summary='&'#" ; else echo "# par_summary="; fi )
@@ -1549,8 +1574,8 @@ $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}"
 set -eo pipefail

 # Check if both outputs are empty, at least one must be passed.
-if [[ -z "\$par_html" ]] && [[ -z "\$par_zip" ]] && [[ -z "\$par_summary" ]] && [[ -z "\$par_data" ]]; then
-  echo "Error: At least one of the output arguments (--html, --zip, --summary, and --data) must be passed."
+if [[ -z "\$par_outdir" ]] && [[ -z "\$par_html" ]] && [[ -z "\$par_zip" ]] && [[ -z "\$par_summary" ]] && [[ -z "\$par_data" ]]; then
+  echo "Error: At least one of the output arguments (--outdir, --html, --zip, --summary, and --data) must be passed."
  exit 1
 fi

@@ -1576,6 +1601,16 @@ function clean_up {
 }
 trap clean_up EXIT

+# Set output directory
+if [[ -n "\$par_outdir" ]]; then
+  if [[ ! -d "\$par_outdir" ]]; then
+    mkdir -p "\$par_outdir"
+  fi
+  output_dir="\$par_outdir"
+else
+  output_dir="\$tmpdir"
+fi
+
 # Create input array 
 IFS=";" read -ra input <<< \$par_input

@@ -1595,35 +1630,50 @@ fastqc \\
  \${par_quiet:+--quiet} \\
  \${meta_cpus:+--threads "\$meta_cpus"} \\
  \${meta_temp_dir:+--dir "\$meta_temp_dir"} \\
-  --outdir "\${tmpdir}" \\
+  --outdir "\${output_dir}" \\
  "\${input[@]}"
 
+
 # Move output files
 for file in "\${input[@]}"; do
-  # Removes everthing after the first dot of the basename
+  # Removes everything after the first dot of the basename
  sample_name=\$(basename "\${file}" | sed 's/\\..*\$//')
  if [[ -n "\$par_html" ]]; then
-    input_html="\${tmpdir}/\${sample_name}_fastqc.html"
-    html_file="\${par_html//\\*/\$sample_name}"
-    mv "\$input_html" "\$html_file"
+    input_html="\${output_dir}/\${sample_name}_fastqc.html"
+    if [[ ! -f "\$input_html" ]]; then
+      echo "WARNING: HTML file '\$input_html' does not exist"
+    else
+      html_file="\${par_html//\\*/\$sample_name}"
+      cp "\$input_html" "\$html_file"
+    fi
  fi
  if [[ -n "\$par_zip" ]]; then
-    input_zip="\${tmpdir}/\${sample_name}_fastqc.zip"
-    zip_file="\${par_zip//\\*/\$sample_name}"
-    mv "\$input_zip" "\$zip_file"
+    input_zip="\${output_dir}/\${sample_name}_fastqc.zip"
+    if [[ ! -f "\$input_zip" ]]; then
+      echo "WARNING: ZIP file '\$input_zip' does not exist"
+    else
+      zip_file="\${par_zip//\\*/\$sample_name}"
+      cp "\$input_zip" "\$zip_file"
+    fi
  fi
  if [[ -n "\$par_summary" ]]; then
-    summary_file="\${tmpdir}/\${sample_name}_fastqc/summary.txt"
-    new_summary="\${par_summary//\\*/\$sample_name}"
-    mv "\$summary_file" "\$new_summary"
+    summary_file="\${output_dir}/\${sample_name}_fastqc/summary.txt"
+    if [[ ! -f "\$summary_file" ]]; then
+      echo "WARNING: Summary file '\$summary_file' does not exist"
+    else
+      new_summary="\${par_summary//\\*/\$sample_name}"
+      cp "\$summary_file" "\$new_summary"
+    fi
  fi
  if [[ -n "\$par_data" ]]; then
-    data_file="\${tmpdir}/\${sample_name}_fastqc/fastqc_data.txt"
-    new_data="\${par_data//\\*/\$sample_name}"
-    mv "\$data_file" "\$new_data"
+    data_file="\${output_dir}/\${sample_name}_fastqc/fastqc_data.txt"
+    if [[ ! -f "\$data_file" ]]; then
+      echo "WARNING: Data file '\$data_file' does not exist"
+    else
+      new_data="\${par_data//\\*/\$sample_name}"
+      cp "\$data_file" "\$new_data"
+    fi
  fi
-  # Remove the extracted directory
-  rm -r "\${tmpdir}/\${sample_name}_fastqc"
 done
 VIASHMAIN
 bash "\$tempscript" &
@@ -1648,6 +1698,9 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
    done
    VIASH_PAR_INPUT="$VIASH_TEST_INPUT"
  fi
+  if [ ! -z "$VIASH_PAR_OUTDIR" ]; then
+    VIASH_PAR_OUTDIR=$(ViashDockerStripAutomount "$VIASH_PAR_OUTDIR")
+  fi
  if [ ! -z "$VIASH_PAR_HTML" ]; then
    VIASH_PAR_HTML=$(ViashDockerStripAutomount "$VIASH_PAR_HTML")
  fi
@@ -1685,6 +1738,10 @@ fi


 # check whether required files exist
+if [ ! -z "$VIASH_PAR_OUTDIR" ] && [ ! -e "$VIASH_PAR_OUTDIR" ]; then
+  ViashError "Output file '$VIASH_PAR_OUTDIR' does not exist."
+  exit 1
+fi
 if [ ! -z "$VIASH_PAR_HTML" ] && ! compgen -G "$VIASH_PAR_HTML" > /dev/null; then
  ViashError "Output file '$VIASH_PAR_HTML' does not exist."
  exit 1