Build branch main with version main (ec69d9a)

Build pipeline: viash-hub.biobox.main-t2txs

Source commit: ec69d9af7a

Source message: FEAT: update busco to 5.7.1 (#72)

* FEAT: update busco to 5.7.1

* Typo

target/executable/busco/busco_run/.config.vsh.yaml

@@ -263,6 +263,11 @@ argument_groups:
     direction: "input"
 - name: "MetaEuk Settings"
   arguments:
+  - type: "boolean_true"
+    name: "--metaeuk"
+    description: "Use Metaeuk gene predictor.\n"
+    info: null
+    direction: "input"
   - type: "string"
     name: "--metaeuk_parameters"
     description: "Pass additional arguments to Metaeuk for the first run (see Metaeuk\
@@ -385,7 +390,7 @@ runners:
 engines:
 - type: "docker"
   id: "docker"
-  image: "quay.io/biocontainers/busco:5.6.1--pyhdfd78af_0"
+  image: "quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0"
   target_registry: "images.viash-hub.com"
   target_tag: "main"
   namespace_separator: "/"
@@ -404,7 +409,7 @@ build_info:
   output: "target/executable/busco/busco_run"
   executable: "target/executable/busco/busco_run/busco_run"
   viash_version: "0.9.0-RC6"
-  git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+  git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"

target/executable/busco/busco_run/busco_run

@@ -329,6 +329,10 @@ function ViashHelp {
   echo "        Use Miniprot gene predictor."
   echo ""
   echo "MetaEuk Settings:"
+  echo "    --metaeuk"
+  echo "        type: boolean_true"
+  echo "        Use Metaeuk gene predictor."
+  echo ""
   echo "    --metaeuk_parameters"
   echo "        type: string"
   echo "        example: --max-overlap=15,--min-exon-aa=15"
@@ -618,14 +622,14 @@ function ViashDockerfile {
 
   if [[ "$engine_id" == "docker" ]]; then
     cat << 'VIASHDOCKER'
-FROM quay.io/biocontainers/busco:5.6.1--pyhdfd78af_0
+FROM quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0
 ENTRYPOINT []
 RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.description="Companion container for running component busco busco_run"
-LABEL org.opencontainers.image.created="2024-07-01T10:12:50Z"
+LABEL org.opencontainers.image.created="2024-07-01T20:00:31Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -989,6 +993,11 @@ while [[ $# -gt 0 ]]; do
             VIASH_PAR_MINIPROT=true
             shift 1
             ;;
+        --metaeuk)
+            [ -n "$VIASH_PAR_METAEUK" ] && ViashError Bad arguments for option \'--metaeuk\': \'$VIASH_PAR_METAEUK\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_METAEUK=true
+            shift 1
+            ;;
         --metaeuk_parameters)
             [ -n "$VIASH_PAR_METAEUK_PARAMETERS" ] && ViashError Bad arguments for option \'--metaeuk_parameters\': \'$VIASH_PAR_METAEUK_PARAMETERS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
             VIASH_PAR_METAEUK_PARAMETERS="$2"
@@ -1234,6 +1243,9 @@ fi
 if [ -z ${VIASH_PAR_MINIPROT+x} ]; then
   VIASH_PAR_MINIPROT="false"
 fi
+if [ -z ${VIASH_PAR_METAEUK+x} ]; then
+  VIASH_PAR_METAEUK="false"
+fi
 
 # check whether required files exist
 if [ ! -z "$VIASH_PAR_INPUT" ] && [ ! -e "$VIASH_PAR_INPUT" ]; then
@@ -1326,6 +1338,12 @@ if [[ -n "$VIASH_PAR_MINIPROT" ]]; then
     exit 1
   fi
 fi
+if [[ -n "$VIASH_PAR_METAEUK" ]]; then
+  if ! [[ "$VIASH_PAR_METAEUK" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--metaeuk' has to be a boolean_true. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
 if [[ -n "$VIASH_META_CPUS" ]]; then
   if ! [[ "$VIASH_META_CPUS" =~ ^[-+]?[0-9]+$ ]]; then
     ViashError 'cpus' has to be an integer. Use "--help" to get more information on the parameters.
@@ -1566,6 +1584,7 @@ $( if [ ! -z ${VIASH_PAR_LIMIT+x} ]; then echo "${VIASH_PAR_LIMIT}" | sed "s#'#'
 $( if [ ! -z ${VIASH_PAR_SCAFFOLD_COMPOSITION+x} ]; then echo "${VIASH_PAR_SCAFFOLD_COMPOSITION}" | sed "s#'#'\"'\"'#g;s#.*#par_scaffold_composition='&'#" ; else echo "# par_scaffold_composition="; fi )
 $( if [ ! -z ${VIASH_PAR_E_VALUE+x} ]; then echo "${VIASH_PAR_E_VALUE}" | sed "s#'#'\"'\"'#g;s#.*#par_e_value='&'#" ; else echo "# par_e_value="; fi )
 $( if [ ! -z ${VIASH_PAR_MINIPROT+x} ]; then echo "${VIASH_PAR_MINIPROT}" | sed "s#'#'\"'\"'#g;s#.*#par_miniprot='&'#" ; else echo "# par_miniprot="; fi )
+$( if [ ! -z ${VIASH_PAR_METAEUK+x} ]; then echo "${VIASH_PAR_METAEUK}" | sed "s#'#'\"'\"'#g;s#.*#par_metaeuk='&'#" ; else echo "# par_metaeuk="; fi )
 $( if [ ! -z ${VIASH_PAR_METAEUK_PARAMETERS+x} ]; then echo "${VIASH_PAR_METAEUK_PARAMETERS}" | sed "s#'#'\"'\"'#g;s#.*#par_metaeuk_parameters='&'#" ; else echo "# par_metaeuk_parameters="; fi )
 $( if [ ! -z ${VIASH_PAR_METAEUK_RERUN_PARAMETERS+x} ]; then echo "${VIASH_PAR_METAEUK_RERUN_PARAMETERS}" | sed "s#'#'\"'\"'#g;s#.*#par_metaeuk_rerun_parameters='&'#" ; else echo "# par_metaeuk_rerun_parameters="; fi )
 $( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi )
@@ -1625,6 +1644,7 @@ busco \\
     \${par_force:+--force} \\
     \${par_limit:+--limit "\$par_limit"} \\
     \${par_long:+--long} \\
+    \${par_metaeuk:+--metaeuk} \\
     \${par_metaeuk_parameters:+--metaeuk_parameters "\$par_metaeuk_parameters"} \\
     \${par_metaeuk_rerun_parameters:+--metaeuk_rerun_parameters "\$par_metaeuk_rerun_parameters"} \\
     \${par_miniprot:+--miniprot} \\