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
2024-07-01 20:19:17 +00:00
parent bece67ad47
commit ae3fef8eec
125 changed files with 2030 additions and 268 deletions
--- a/target/executable/arriba/.config.vsh.yaml
+++ b/target/executable/arriba/.config.vsh.yaml
@@ -688,7 +688,7 @@ build_info:
  output: "target/executable/arriba"
  executable: "target/executable/arriba/arriba"
  viash_version: "0.9.0-RC6"
-  git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+  git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/arriba/arriba
+++ b/target/executable/arriba/arriba
@@ -749,9 +749,9 @@ ENTRYPOINT []
 RUN arriba -h | grep 'Version:' 2>&1 |  sed 's/Version:\s\(.*\)/arriba: "\1"/' > /var/software_versions.txt

 LABEL org.opencontainers.image.description="Companion container for running component arriba"
-LABEL org.opencontainers.image.created="2024-07-01T10:12:56Z"
+LABEL org.opencontainers.image.created="2024-07-01T20:00:37Z"
 LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba"
-LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bcl_convert/.config.vsh.yaml
+++ b/target/executable/bcl_convert/.config.vsh.yaml
@@ -386,7 +386,7 @@ build_info:
  output: "target/executable/bcl_convert"
  executable: "target/executable/bcl_convert/bcl_convert"
  viash_version: "0.9.0-RC6"
-  git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+  git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/bcl_convert/bcl_convert
+++ b/target/executable/bcl_convert/bcl_convert
@@ -593,9 +593,9 @@ rm /tmp/bcl-convert.rpm
 RUN echo "bcl-convert: \"$(bcl-convert -V 2>&1 >/dev/null | sed -n '/Version/ s/^bcl-convert\ Version //p')\"" > /var/software_versions.txt

 LABEL org.opencontainers.image.description="Companion container for running component bcl_convert"
-LABEL org.opencontainers.image.created="2024-07-01T10:12:54Z"
+LABEL org.opencontainers.image.created="2024-07-01T20:00:36Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml
@@ -217,7 +217,7 @@ build_info:
  output: "target/executable/bedtools/bedtools_getfasta"
  executable: "target/executable/bedtools/bedtools_getfasta/bedtools_getfasta"
  viash_version: "0.9.0-RC6"
-  git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+  git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta
+++ b/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta
@@ -521,9 +521,9 @@ RUN apt-get update && \
 RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var/software_versions.txt

 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_getfasta"
-LABEL org.opencontainers.image.created="2024-07-01T10:12:54Z"
+LABEL org.opencontainers.image.created="2024-07-01T20:00:35Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/busco/busco_download_datasets/.config.vsh.yaml
+++ b/target/executable/busco/busco_download_datasets/.config.vsh.yaml
@@ -125,7 +125,7 @@ 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: "/"
@@ -144,7 +144,7 @@ build_info:
  output: "target/executable/busco/busco_download_datasets"
  executable: "target/executable/busco/busco_download_datasets/busco_download_datasets"
  viash_version: "0.9.0-RC6"
-  git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+  git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/busco/busco_download_datasets/busco_download_datasets
+++ b/target/executable/busco/busco_download_datasets/busco_download_datasets
@@ -465,14 +465,14 @@ 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_download_datasets"
-LABEL org.opencontainers.image.created="2024-07-01T10:12:49Z"
+LABEL org.opencontainers.image.created="2024-07-01T20:00:30Z"
 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
--- a/target/executable/busco/busco_list_datasets/.config.vsh.yaml
+++ b/target/executable/busco/busco_list_datasets/.config.vsh.yaml
@@ -112,7 +112,7 @@ 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: "/"
@@ -131,7 +131,7 @@ build_info:
  output: "target/executable/busco/busco_list_datasets"
  executable: "target/executable/busco/busco_list_datasets/busco_list_datasets"
  viash_version: "0.9.0-RC6"
-  git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+  git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/busco/busco_list_datasets/busco_list_datasets
+++ b/target/executable/busco/busco_list_datasets/busco_list_datasets
@@ -455,14 +455,14 @@ 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_list_datasets"
-LABEL org.opencontainers.image.created="2024-07-01T10:12:49Z"
+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
--- a/target/executable/busco/busco_run/.config.vsh.yaml
+++ b/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"
--- a/target/executable/busco/busco_run/busco_run
+++ b/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} \\
--- a/target/executable/cutadapt/.config.vsh.yaml
+++ b/target/executable/cutadapt/.config.vsh.yaml
@@ -305,6 +305,26 @@ argument_groups:
      \ If match is on reverse-complemented version,\noutput that one.\n"
    info: null
    direction: "input"
+- name: "Demultiplexing options"
+  arguments:
+  - type: "string"
+    name: "--demultiplex_mode"
+    description: "Enable demultiplexing and set the mode for it.\nWith mode 'unique_dual',\
+      \ adapters from the first and second read are used,\nand the indexes from the\
+      \ reads are only used in pairs. This implies\n--pair_adapters.\nEnabling mode\
+      \ 'combinatorial_dual' allows all combinations of the sets of indexes\non R1\
+      \ and R2. It is necessary to write each read pair to an output\nfile depending\
+      \ on the adapters found on both R1 and R2.\nMode 'single', uses indexes or barcodes\
+      \ located at the 5'\nend of the R1 read (single). \n"
+    info: null
+    required: false
+    choices:
+    - "single"
+    - "unique_dual"
+    - "combinatorial_dual"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
 - name: "Read modifications"
  arguments:
  - type: "integer"
@@ -707,7 +727,7 @@ build_info:
  output: "target/executable/cutadapt"
  executable: "target/executable/cutadapt/cutadapt"
  viash_version: "0.9.0-RC6"
-  git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+  git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/cutadapt/cutadapt
+++ b/target/executable/cutadapt/cutadapt
@@ -357,6 +357,22 @@ function ViashHelp {
  echo "        matches. If match is on reverse-complemented version,"
  echo "        output that one."
  echo ""
+  echo "Demultiplexing options:"
+  echo "    --demultiplex_mode"
+  echo "        type: string"
+  echo "        choices: [ single, unique_dual, combinatorial_dual ]"
+  echo "        Enable demultiplexing and set the mode for it."
+  echo "        With mode 'unique_dual', adapters from the first and second read are"
+  echo "        used,"
+  echo "        and the indexes from the reads are only used in pairs. This implies"
+  echo "        --pair_adapters."
+  echo "        Enabling mode 'combinatorial_dual' allows all combinations of the sets"
+  echo "        of indexes"
+  echo "        on R1 and R2. It is necessary to write each read pair to an output"
+  echo "        file depending on the adapters found on both R1 and R2."
+  echo "        Mode 'single', uses indexes or barcodes located at the 5'"
+  echo "        end of the R1 read (single)."
+  echo ""
  echo "Read modifications:"
  echo "    -u, --cut"
  echo "        type: integer, multiple values allowed"
@@ -810,9 +826,9 @@ RUN pip install --upgrade pip && \
 RUN cutadapt --version | sed 's/\(.*\)/cutadapt: "\1"/' > /var/software_versions.txt

 LABEL org.opencontainers.image.description="Companion container for running component cutadapt"
-LABEL org.opencontainers.image.created="2024-07-01T10:12:46Z"
+LABEL org.opencontainers.image.created="2024-07-01T20:00:27Z"
 LABEL org.opencontainers.image.source="https://github.com/marcelm/cutadapt"
-LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
@@ -1303,6 +1319,17 @@ while [[ $# -gt 0 ]]; do
            VIASH_PAR_REVCOMP=true
            shift 1
            ;;
+        --demultiplex_mode)
+            [ -n "$VIASH_PAR_DEMULTIPLEX_MODE" ] && ViashError Bad arguments for option \'--demultiplex_mode\': \'$VIASH_PAR_DEMULTIPLEX_MODE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_DEMULTIPLEX_MODE="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --demultiplex_mode. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --demultiplex_mode=*)
+            [ -n "$VIASH_PAR_DEMULTIPLEX_MODE" ] && ViashError Bad arguments for option \'--demultiplex_mode=*\': \'$VIASH_PAR_DEMULTIPLEX_MODE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_DEMULTIPLEX_MODE=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
        --cut)
            if [ -z "$VIASH_PAR_CUT" ]; then
              VIASH_PAR_CUT="$2"
@@ -2202,6 +2229,18 @@ if [ ! -z "$VIASH_PAR_ACTION" ]; then
  unset IFS
 fi

+if [ ! -z "$VIASH_PAR_DEMULTIPLEX_MODE" ]; then
+  VIASH_PAR_DEMULTIPLEX_MODE_CHOICES=("single;unique_dual;combinatorial_dual")
+  IFS=';'
+  set -f
+  if ! [[ ";${VIASH_PAR_DEMULTIPLEX_MODE_CHOICES[*]};" =~ ";$VIASH_PAR_DEMULTIPLEX_MODE;" ]]; then
+    ViashError '--demultiplex_mode' specified value of \'$VIASH_PAR_DEMULTIPLEX_MODE\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+  set +f
+  unset IFS
+fi
+
 if [ ! -z "$VIASH_PAR_REPORT" ]; then
  VIASH_PAR_REPORT_CHOICES=("full;minimal")
  IFS=';'
@@ -2378,6 +2417,7 @@ $( if [ ! -z ${VIASH_PAR_MATCH_READ_WILDCARDS+x} ]; then echo "${VIASH_PAR_MATCH
 $( if [ ! -z ${VIASH_PAR_NO_MATCH_ADAPTER_WILDCARDS+x} ]; then echo "${VIASH_PAR_NO_MATCH_ADAPTER_WILDCARDS}" | sed "s#'#'\"'\"'#g;s#.*#par_no_match_adapter_wildcards='&'#" ; else echo "# par_no_match_adapter_wildcards="; fi )
 $( if [ ! -z ${VIASH_PAR_ACTION+x} ]; then echo "${VIASH_PAR_ACTION}" | sed "s#'#'\"'\"'#g;s#.*#par_action='&'#" ; else echo "# par_action="; fi )
 $( if [ ! -z ${VIASH_PAR_REVCOMP+x} ]; then echo "${VIASH_PAR_REVCOMP}" | sed "s#'#'\"'\"'#g;s#.*#par_revcomp='&'#" ; else echo "# par_revcomp="; fi )
+$( if [ ! -z ${VIASH_PAR_DEMULTIPLEX_MODE+x} ]; then echo "${VIASH_PAR_DEMULTIPLEX_MODE}" | sed "s#'#'\"'\"'#g;s#.*#par_demultiplex_mode='&'#" ; else echo "# par_demultiplex_mode="; fi )
 $( if [ ! -z ${VIASH_PAR_CUT+x} ]; then echo "${VIASH_PAR_CUT}" | sed "s#'#'\"'\"'#g;s#.*#par_cut='&'#" ; else echo "# par_cut="; fi )
 $( if [ ! -z ${VIASH_PAR_CUT_R2+x} ]; then echo "${VIASH_PAR_CUT_R2}" | sed "s#'#'\"'\"'#g;s#.*#par_cut_r2='&'#" ; else echo "# par_cut_r2="; fi )
 $( if [ ! -z ${VIASH_PAR_NEXTSEQ_TRIM+x} ]; then echo "${VIASH_PAR_NEXTSEQ_TRIM}" | sed "s#'#'\"'\"'#g;s#.*#par_nextseq_trim='&'#" ; else echo "# par_nextseq_trim="; fi )
@@ -2545,7 +2585,7 @@ mod_args=\$(echo \\
  \${par_cut_r2:+--cut_r2 "\${par_cut_r2}"} \\
  \${par_nextseq_trim:+--nextseq-trim "\${par_nextseq_trim}"} \\
  \${par_quality_cutoff:+--quality-cutoff "\${par_quality_cutoff}"} \\
-  \${par_quality_cutoff_r2:+--quality-cutoff_r2 "\${par_quality_cutoff_r2}"} \\
+  \${par_quality_cutoff_r2:+-Q "\${par_quality_cutoff_r2}"} \\
  \${par_quality_base:+--quality-base "\${par_quality_base}"} \\
  \${par_poly_a:+--poly-a} \\
  \${par_length:+--length "\${par_length}"} \\
@@ -2614,14 +2654,35 @@ else
  ext="fasta"
 fi

-if [ \$mode = "se" ]; then
+demultiplex_mode="\$par_demultiplex_mode"
+if [[ \$mode == "se" ]]; then
+  if [[ "\$demultiplex_mode" == "unique_dual" ]] || [[ "\$demultiplex_mode" == "combinatorial_dual" ]]; then
+    echo "Demultiplexing dual indexes is not possible with single-end data."
+    exit 1
+  fi
+  prefix="trimmed_"
+  if [[ ! -z "\$demultiplex_mode" ]]; then
+    prefix="{name}_"
+  fi
  output_args=\$(echo \\
-    --output "\$output_dir/{name}_001.\$ext" \\
+    --output "\$output_dir/\${prefix}001.\$ext" \\
  )
 else
+  demultiplex_indicator_r1='{name}_'
+  demultiplex_indicator_r2=\$demultiplex_indicator_r1
+  if [[ "\$demultiplex_mode" == "combinatorial_dual" ]]; then
+    demultiplex_indicator_r1='{name1}_{name2}_'
+    demultiplex_indicator_r2='{name1}_{name2}_'
+  fi
+  prefix_r1="trimmed_"
+  prefix_r2="trimmed_"
+  if [[ ! -z "\$demultiplex_mode" ]]; then
+    prefix_r1=\$demultiplex_indicator_r1
+    prefix_r2=\$demultiplex_indicator_r2
+  fi
  output_args=\$(echo \\
-    --output "\$output_dir/{name}_R1_001.\$ext" \\
-    --paired-output "\$output_dir/{name}_R2_001.\$ext" \\
+    --output "\$output_dir/\${prefix_r1}R1_001.\$ext" \\
+    --paired-output "\$output_dir/\${prefix_r2}R2_001.\$ext" \\
  )
 fi

--- a/target/executable/falco/.config.vsh.yaml
+++ b/target/executable/falco/.config.vsh.yaml
@@ -304,7 +304,7 @@ build_info:
  output: "target/executable/falco"
  executable: "target/executable/falco/falco"
  viash_version: "0.9.0-RC6"
-  git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+  git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/falco/falco
+++ b/target/executable/falco/falco
@@ -584,9 +584,9 @@ make install
 RUN echo "falco: \"$(falco -v | sed -n 's/^falco //p')\"" > /var/software_versions.txt

 LABEL org.opencontainers.image.description="Companion container for running component falco"
-LABEL org.opencontainers.image.created="2024-07-01T10:12:46Z"
+LABEL org.opencontainers.image.created="2024-07-01T20:00:27Z"
 LABEL org.opencontainers.image.source="https://github.com/smithlabcode/falco"
-LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/fastp/.config.vsh.yaml
+++ b/target/executable/fastp/.config.vsh.yaml
@@ -1065,7 +1065,7 @@ build_info:
  output: "target/executable/fastp"
  executable: "target/executable/fastp/fastp"
  viash_version: "0.9.0-RC6"
-  git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+  git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/fastp/fastp
+++ b/target/executable/fastp/fastp
@@ -1023,9 +1023,9 @@ ENTRYPOINT []
 RUN fastp --version 2>&1 | sed 's# #: "#;s#$#"#' > /var/software_versions.txt

 LABEL org.opencontainers.image.description="Companion container for running component fastp"
-LABEL org.opencontainers.image.created="2024-07-01T10:12:47Z"
+LABEL org.opencontainers.image.created="2024-07-01T20:00:28Z"
 LABEL org.opencontainers.image.source="https://github.com/OpenGene/fastp"
-LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/featurecounts/.config.vsh.yaml
+++ b/target/executable/featurecounts/.config.vsh.yaml
@@ -631,7 +631,7 @@ build_info:
  output: "target/executable/featurecounts"
  executable: "target/executable/featurecounts/featurecounts"
  viash_version: "0.9.0-RC6"
-  git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+  git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/featurecounts/featurecounts
+++ b/target/executable/featurecounts/featurecounts
@@ -749,9 +749,9 @@ ENTRYPOINT []
 RUN featureCounts -v 2>&1 | sed 's/featureCounts v\([0-9.]*\)/featureCounts: \1/' > /var/software_versions.txt

 LABEL org.opencontainers.image.description="Companion container for running component featurecounts"
-LABEL org.opencontainers.image.created="2024-07-01T10:12:56Z"
+LABEL org.opencontainers.image.created="2024-07-01T20:00:37Z"
 LABEL org.opencontainers.image.source="https://github.com/ShiLab-Bioinformatics/subread"
-LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/gffread/.config.vsh.yaml
+++ b/target/executable/gffread/.config.vsh.yaml
@@ -671,7 +671,7 @@ build_info:
  output: "target/executable/gffread"
  executable: "target/executable/gffread/gffread"
  viash_version: "0.9.0-RC6"
-  git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+  git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/gffread/gffread
+++ b/target/executable/gffread/gffread
@@ -802,9 +802,9 @@ ENTRYPOINT []
 RUN echo "gffread: \"$(gffread --version 2>&1)\"" > /var/software_versions.txt

 LABEL org.opencontainers.image.description="Companion container for running component gffread"
-LABEL org.opencontainers.image.created="2024-07-01T10:12:47Z"
+LABEL org.opencontainers.image.created="2024-07-01T20:00:28Z"
 LABEL org.opencontainers.image.source="https://github.com/gpertea/gffread"
-LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/lofreq/lofreq_call/.config.vsh.yaml
+++ b/target/executable/lofreq/lofreq_call/.config.vsh.yaml
@@ -489,7 +489,7 @@ build_info:
  output: "target/executable/lofreq/lofreq_call"
  executable: "target/executable/lofreq/lofreq_call/lofreq_call"
  viash_version: "0.9.0-RC6"
-  git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+  git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/lofreq/lofreq_call/lofreq_call
+++ b/target/executable/lofreq/lofreq_call/lofreq_call
@@ -651,9 +651,9 @@ RUN version=$(lofreq version | grep 'version' | sed 's/version: //') && \
 echo "lofreq: $version" > /var/software_versions.txt

 LABEL org.opencontainers.image.description="Companion container for running component lofreq lofreq_call"
-LABEL org.opencontainers.image.created="2024-07-01T10:12:50Z"
+LABEL org.opencontainers.image.created="2024-07-01T20:00:32Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml
+++ b/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml
@@ -197,7 +197,7 @@ build_info:
  output: "target/executable/lofreq/lofreq_indelqual"
  executable: "target/executable/lofreq/lofreq_indelqual/lofreq_indelqual"
  viash_version: "0.9.0-RC6"
-  git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+  git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual
+++ b/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual
@@ -496,9 +496,9 @@ RUN version=$(lofreq version | grep 'version' | sed 's/version: //') && \
 echo "lofreq: $version" > /var/software_versions.txt

 LABEL org.opencontainers.image.description="Companion container for running component lofreq lofreq_indelqual"
-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://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/multiqc/.config.vsh.yaml
+++ b/target/executable/multiqc/.config.vsh.yaml
@@ -438,7 +438,7 @@ build_info:
  output: "target/executable/multiqc"
  executable: "target/executable/multiqc/multiqc"
  viash_version: "0.9.0-RC6"
-  git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+  git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/multiqc/multiqc
+++ b/target/executable/multiqc/multiqc
@@ -632,9 +632,9 @@ ENTRYPOINT []
 RUN multiqc --version | sed 's/multiqc, version\s\(.*\)/multiqc: "\1"/' > /var/software_versions.txt

 LABEL org.opencontainers.image.description="Companion container for running component multiqc"
-LABEL org.opencontainers.image.created="2024-07-01T10:12:45Z"
+LABEL org.opencontainers.image.created="2024-07-01T20:00:27Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/pear/.config.vsh.yaml
+++ b/target/executable/pear/.config.vsh.yaml
@@ -380,7 +380,7 @@ build_info:
  output: "target/executable/pear"
  executable: "target/executable/pear/pear"
  viash_version: "0.9.0-RC6"
-  git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+  git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/pear/pear
+++ b/target/executable/pear/pear
@@ -592,9 +592,9 @@ RUN version=$(pear -h | grep 'PEAR v' | sed 's/PEAR v//' | sed 's/ .*//') && \
 echo "pear: $version" > /var/software_versions.txt

 LABEL org.opencontainers.image.description="Companion container for running component pear"
-LABEL org.opencontainers.image.created="2024-07-01T10:12:54Z"
+LABEL org.opencontainers.image.created="2024-07-01T20:00:35Z"
 LABEL org.opencontainers.image.source="https://github.com/tseemann/PEAR"
-LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/salmon/salmon_index/.config.vsh.yaml
+++ b/target/executable/salmon/salmon_index/.config.vsh.yaml
@@ -263,7 +263,7 @@ build_info:
  output: "target/executable/salmon/salmon_index"
  executable: "target/executable/salmon/salmon_index/salmon_index"
  viash_version: "0.9.0-RC6"
-  git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+  git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/salmon/salmon_index/salmon_index
+++ b/target/executable/salmon/salmon_index/salmon_index
@@ -541,9 +541,9 @@ ENTRYPOINT []
 RUN salmon index -v 2>&1 | sed 's/salmon \([0-9.]*\)/salmon: \1/' > /var/software_versions.txt

 LABEL org.opencontainers.image.description="Companion container for running component salmon salmon_index"
-LABEL org.opencontainers.image.created="2024-07-01T10:12:55Z"
+LABEL org.opencontainers.image.created="2024-07-01T20:00:36Z"
 LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
-LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/salmon/salmon_quant/.config.vsh.yaml
+++ b/target/executable/salmon/salmon_quant/.config.vsh.yaml
@@ -1159,7 +1159,7 @@ build_info:
  output: "target/executable/salmon/salmon_quant"
  executable: "target/executable/salmon/salmon_quant/salmon_quant"
  viash_version: "0.9.0-RC6"
-  git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+  git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/salmon/salmon_quant/salmon_quant
+++ b/target/executable/salmon/salmon_quant/salmon_quant
@@ -1163,9 +1163,9 @@ ENTRYPOINT []
 RUN salmon index -v 2>&1 | sed 's/salmon \([0-9.]*\)/salmon: \1/' > /var/software_versions.txt

 LABEL org.opencontainers.image.description="Companion container for running component salmon salmon_quant"
-LABEL org.opencontainers.image.created="2024-07-01T10:12:55Z"
+LABEL org.opencontainers.image.created="2024-07-01T20:00:36Z"
 LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
-LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_collate/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_collate/.config.vsh.yaml
@@ -250,7 +250,7 @@ build_info:
  output: "target/executable/samtools/samtools_collate"
  executable: "target/executable/samtools/samtools_collate/samtools_collate"
  viash_version: "0.9.0-RC6"
-  git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+  git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_collate/samtools_collate
+++ b/target/executable/samtools/samtools_collate/samtools_collate
@@ -514,9 +514,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
 sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt

 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_collate"
-LABEL org.opencontainers.image.created="2024-07-01T10:12:52Z"
+LABEL org.opencontainers.image.created="2024-07-01T20:00:33Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_faidx/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_faidx/.config.vsh.yaml
@@ -229,7 +229,7 @@ build_info:
  output: "target/executable/samtools/samtools_faidx"
  executable: "target/executable/samtools/samtools_faidx/samtools_faidx"
  viash_version: "0.9.0-RC6"
-  git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+  git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_faidx/samtools_faidx
+++ b/target/executable/samtools/samtools_faidx/samtools_faidx
@@ -507,9 +507,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
 sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt

 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_faidx"
-LABEL org.opencontainers.image.created="2024-07-01T10:12:53Z"
+LABEL org.opencontainers.image.created="2024-07-01T20:00:34Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_fastq/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_fastq/.config.vsh.yaml
@@ -417,7 +417,7 @@ build_info:
  output: "target/executable/samtools/samtools_fastq"
  executable: "target/executable/samtools/samtools_fastq/samtools_fastq"
  viash_version: "0.9.0-RC6"
-  git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+  git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_fastq/samtools_fastq
+++ b/target/executable/samtools/samtools_fastq/samtools_fastq
@@ -620,9 +620,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
 sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt

 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_fastq"
-LABEL org.opencontainers.image.created="2024-07-01T10:12:51Z"
+LABEL org.opencontainers.image.created="2024-07-01T20:00:33Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_flagstat/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_flagstat/.config.vsh.yaml
@@ -159,7 +159,7 @@ build_info:
  output: "target/executable/samtools/samtools_flagstat"
  executable: "target/executable/samtools/samtools_flagstat/samtools_flagstat"
  viash_version: "0.9.0-RC6"
-  git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+  git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_flagstat/samtools_flagstat
+++ b/target/executable/samtools/samtools_flagstat/samtools_flagstat
@@ -469,9 +469,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
 sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt

 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_flagstat"
-LABEL org.opencontainers.image.created="2024-07-01T10:12:53Z"
+LABEL org.opencontainers.image.created="2024-07-01T20:00:34Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_idxstats/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_idxstats/.config.vsh.yaml
@@ -169,7 +169,7 @@ build_info:
  output: "target/executable/samtools/samtools_idxstats"
  executable: "target/executable/samtools/samtools_idxstats/samtools_idxstats"
  viash_version: "0.9.0-RC6"
-  git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+  git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_idxstats/samtools_idxstats
+++ b/target/executable/samtools/samtools_idxstats/samtools_idxstats
@@ -473,9 +473,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
 sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt

 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_idxstats"
-LABEL org.opencontainers.image.created="2024-07-01T10:12:52Z"
+LABEL org.opencontainers.image.created="2024-07-01T20:00:34Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_index/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_index/.config.vsh.yaml
@@ -175,7 +175,7 @@ build_info:
  output: "target/executable/samtools/samtools_index"
  executable: "target/executable/samtools/samtools_index/samtools_index"
  viash_version: "0.9.0-RC6"
-  git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+  git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_index/samtools_index
+++ b/target/executable/samtools/samtools_index/samtools_index
@@ -480,9 +480,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
 sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt

 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_index"
-LABEL org.opencontainers.image.created="2024-07-01T10:12:51Z"
+LABEL org.opencontainers.image.created="2024-07-01T20:00:32Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_sort/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_sort/.config.vsh.yaml
@@ -318,7 +318,7 @@ build_info:
  output: "target/executable/samtools/samtools_sort"
  executable: "target/executable/samtools/samtools_sort/samtools_sort"
  viash_version: "0.9.0-RC6"
-  git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+  git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_sort/samtools_sort
+++ b/target/executable/samtools/samtools_sort/samtools_sort
@@ -551,9 +551,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
 sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt

 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_sort"
-LABEL org.opencontainers.image.created="2024-07-01T10:12:53Z"
+LABEL org.opencontainers.image.created="2024-07-01T20:00:35Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_stats/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_stats/.config.vsh.yaml
@@ -380,7 +380,7 @@ build_info:
  output: "target/executable/samtools/samtools_stats"
  executable: "target/executable/samtools/samtools_stats/samtools_stats"
  viash_version: "0.9.0-RC6"
-  git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+  git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_stats/samtools_stats
+++ b/target/executable/samtools/samtools_stats/samtools_stats
@@ -568,9 +568,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
 sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt

 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_stats"
-LABEL org.opencontainers.image.created="2024-07-01T10:12:52Z"
+LABEL org.opencontainers.image.created="2024-07-01T20:00:33Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_view/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_view/.config.vsh.yaml
@@ -651,7 +651,7 @@ build_info:
  output: "target/executable/samtools/samtools_view"
  executable: "target/executable/samtools/samtools_view/samtools_view"
  viash_version: "0.9.0-RC6"
-  git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+  git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_view/samtools_view
+++ b/target/executable/samtools/samtools_view/samtools_view
@@ -820,9 +820,9 @@ RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
 sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt

 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_view"
-LABEL org.opencontainers.image.created="2024-07-01T10:12:51Z"
+LABEL org.opencontainers.image.created="2024-07-01T20:00:32Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/star/star_align_reads/.config.vsh.yaml
+++ b/target/executable/star/star_align_reads/.config.vsh.yaml
@@ -2108,7 +2108,7 @@ build_info:
  output: "target/executable/star/star_align_reads"
  executable: "target/executable/star/star_align_reads/star_align_reads"
  viash_version: "0.9.0-RC6"
-  git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+  git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/star/star_align_reads/star_align_reads
+++ b/target/executable/star/star_align_reads/star_align_reads
@@ -1665,9 +1665,9 @@ RUN apt-get update && \
 RUN STAR --version | sed 's#\(.*\)#star: "\1"#' > /var/software_versions.txt

 LABEL org.opencontainers.image.description="Companion container for running component star star_align_reads"
-LABEL org.opencontainers.image.created="2024-07-01T10:12:48Z"
+LABEL org.opencontainers.image.created="2024-07-01T20:00:29Z"
 LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR"
-LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/star/star_genome_generate/.config.vsh.yaml
+++ b/target/executable/star/star_genome_generate/.config.vsh.yaml
@@ -319,7 +319,7 @@ build_info:
  output: "target/executable/star/star_genome_generate"
  executable: "target/executable/star/star_genome_generate/star_genome_generate"
  viash_version: "0.9.0-RC6"
-  git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+  git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/star/star_genome_generate/star_genome_generate
+++ b/target/executable/star/star_genome_generate/star_genome_generate
@@ -572,9 +572,9 @@ RUN apt-get update && \
 RUN STAR --version | sed 's#\(.*\)#star: "\1"#' > /var/software_versions.txt

 LABEL org.opencontainers.image.description="Companion container for running component star star_genome_generate"
-LABEL org.opencontainers.image.created="2024-07-01T10:12:48Z"
+LABEL org.opencontainers.image.created="2024-07-01T20:00:29Z"
 LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR"
-LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
+LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER