Build branch main with version main (add1252)

Build pipeline: viash-hub.biobox.main-bv4sf Source commit: add125261c Source message: FEAT: avoid using boolean_false (#160)
2024-10-07 09:26:30 +00:00
parent adf9159264
commit 09f5294af0
268 changed files with 767 additions and 757 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -19,6 +19,10 @@

 ## MINOR CHANGES

+* `agat_convert_bed2gff`: change type of argument `inflate_off` from `boolean_false` to `boolean_true` (PR #160).
+
+* `cutadapt`: change type of argument `no_indels` and `no_match_adapter_wildcards` from `boolean_false` to `boolean_true` (PR #160).
+
 * Upgrade to Viash 0.9.0.

 # biobox 0.2.0
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -231,6 +231,12 @@ Finally, add all other arguments to the config file. There are a few exceptions:

 * If the help lists defaults, do not add them as defaults but to the description. Example: `description: <Explanation of parameter>. Default: 10.`

+Note:
+  
+* Prefer using `boolean_true` over `boolean_false`. This avoids confusion when specifying values for this argument in a Nextflow workflow.
+  For example, consider the CLI option `--no-indels` for `cutadapt`. If the config for `cutadapt` would specify an argument `no_indels` of type `boolean_false`,
+  the script of the component must pass a `--no-indels` argument to `cutadapt` when `par_no_indels` is set to `false`. This becomes problematic setting a value for this argument using `fromState` in a nextflow workflow: with `fromState: ["no_indels": true]`, the value that gets passed to the script is `true` and the `--no-indels` flag would *not* be added to the options for `cutadapt`. This is inconsitent to what one might expect when interpreting `["no_indels": true]`.
+  When using `boolean_true`, the reasoning becomes simpler because its value no longer represents the effect of the argument, but wether or not the flag is set.

 ### Step 10: Add a Docker engine

--- a/src/agat/agat_convert_bed2gff/config.vsh.yaml
+++ b/src/agat/agat_convert_bed2gff/config.vsh.yaml
@@ -49,7 +49,7 @@ argument_groups:
      - name: --inflate_off
        description: |
          By default we inflate the block fields (blockCount, blockSizes, blockStarts) to create subfeatures of the main feature (primary_tag). The type of subfeature created is based on the inflate_type parameter. If you do not want this inflating behaviour you can deactivate it by using the --inflate_off option.
-        type: boolean_false
+        type: boolean_true
      - name: --inflate_type
        description: |
          Feature type (3rd column in gff) created when inflate parameter activated [default: exon].
--- a/src/agat/agat_convert_bed2gff/script.sh
+++ b/src/agat/agat_convert_bed2gff/script.sh
@@ -4,7 +4,7 @@
 ## VIASH END

 # unset flags
-[[ "$par_inflate_off" == "true" ]] && unset par_inflate_off
+[[ "$par_inflate_off" == "false" ]] && unset par_inflate_off
 [[ "$par_verbose" == "false" ]] && unset par_verbose

 # run agat_convert_sp_bed2gff.pl
--- a/src/cutadapt/config.vsh.yaml
+++ b/src/cutadapt/config.vsh.yaml
@@ -196,7 +196,7 @@ argument_groups:
          length of matching region. Default: 0.1 (10%).
        example: 0.1
      - name: --no_indels
-        type: boolean_false
+        type: boolean_true
        description: |
          Allow only mismatches in alignments.

@@ -218,7 +218,7 @@ argument_groups:
        description: |
          Interpret IUPAC wildcards in reads.
      - name: --no_match_adapter_wildcards
-        type: boolean_false
+        type: boolean_true
        description: |
          Do not interpret IUPAC wildcards in adapters.
      - name: --action
--- a/src/cutadapt/script.sh
+++ b/src/cutadapt/script.sh
@@ -96,9 +96,9 @@ debug
 # Input arguments 
 ###########################################################
 echo ">> Parsing input arguments"
-[[ "$par_no_indels" == "true" ]] && unset par_no_indels
+[[ "$par_no_indels" == "false" ]] && unset par_no_indels
 [[ "$par_match_read_wildcards" == "false" ]] && unset par_match_read_wildcards
-[[ "$par_no_match_adapter_wildcards" == "true" ]] && unset par_no_match_adapter_wildcards
+[[ "$par_no_match_adapter_wildcards" == "false" ]] && unset par_no_match_adapter_wildcards
 [[ "$par_revcomp" == "false" ]] && unset par_revcomp

 input_args=$(echo \
--- a/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml
@@ -75,7 +75,7 @@ argument_groups:
    direction: "input"
    multiple: false
    multiple_sep: ";"
-  - type: "boolean_false"
+  - type: "boolean_true"
    name: "--inflate_off"
    description: "By default we inflate the block fields (blockCount, blockSizes,\
      \ blockStarts) to create subfeatures of the main feature (primary_tag). The\
@@ -235,9 +235,9 @@ build_info:
  output: "target/executable/agat/agat_convert_bed2gff"
  executable: "target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff
+++ b/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff
@@ -208,7 +208,7 @@ function ViashHelp {
  echo "        of a gff file. Example: gene, mRNA, CDS, etc. [default: gene]"
  echo ""
  echo "    --inflate_off"
-  echo "        type: boolean_false"
+  echo "        type: boolean_true"
  echo "        By default we inflate the block fields (blockCount, blockSizes,"
  echo "        blockStarts) to create subfeatures of the main feature (primary_tag)."
  echo "        The type of subfeature created is based on the inflate_type parameter."
@@ -515,9 +515,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t

 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_bed2gff"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:46Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:07:56Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
@@ -727,7 +727,7 @@ while [[ $# -gt 0 ]]; do
            ;;
        --inflate_off)
            [ -n "$VIASH_PAR_INFLATE_OFF" ] && ViashError Bad arguments for option \'--inflate_off\': \'$VIASH_PAR_INFLATE_OFF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
-            VIASH_PAR_INFLATE_OFF=false
+            VIASH_PAR_INFLATE_OFF=true
            shift 1
            ;;
        --inflate_type)
@@ -970,7 +970,7 @@ fi

 # filling in defaults
 if [ -z ${VIASH_PAR_INFLATE_OFF+x} ]; then
-  VIASH_PAR_INFLATE_OFF="true"
+  VIASH_PAR_INFLATE_OFF="false"
 fi
 if [ -z ${VIASH_PAR_VERBOSE+x} ]; then
  VIASH_PAR_VERBOSE="false"
@@ -989,7 +989,7 @@ fi
 # check whether parameters values are of the right type
 if [[ -n "$VIASH_PAR_INFLATE_OFF" ]]; then
  if ! [[ "$VIASH_PAR_INFLATE_OFF" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
-    ViashError '--inflate_off' has to be a boolean_false. Use "--help" to get more information on the parameters.
+    ViashError '--inflate_off' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
 fi
@@ -1203,7 +1203,7 @@ $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}"
 ## VIASH END

 # unset flags
-[[ "\$par_inflate_off" == "true" ]] && unset par_inflate_off
+[[ "\$par_inflate_off" == "false" ]] && unset par_inflate_off
 [[ "\$par_verbose" == "false" ]] && unset par_verbose

 # run agat_convert_sp_bed2gff.pl
--- a/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml
@@ -225,9 +225,9 @@ build_info:
  output: "target/executable/agat/agat_convert_embl2gff"
  executable: "target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff
+++ b/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff
@@ -505,9 +505,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t

 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_embl2gff"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:46Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:07:56Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/agat/agat_convert_genscan2gff/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_genscan2gff/.config.vsh.yaml
@@ -230,9 +230,9 @@ build_info:
  output: "target/executable/agat/agat_convert_genscan2gff"
  executable: "target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff
+++ b/target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff
@@ -514,9 +514,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t

 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_genscan2gff"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:47Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:07:57Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml
@@ -228,9 +228,9 @@ build_info:
  output: "target/executable/agat/agat_convert_sp_gff2gtf"
  executable: "target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf
+++ b/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf
@@ -519,9 +519,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t

 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_sp_gff2gtf"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:47Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:07:56Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml
@@ -188,9 +188,9 @@ build_info:
  output: "target/executable/agat/agat_convert_sp_gff2tsv"
  executable: "target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv
+++ b/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv
@@ -484,9 +484,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t

 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_sp_gff2tsv"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:46Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:07:55Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml
@@ -195,9 +195,9 @@ build_info:
  output: "target/executable/agat/agat_convert_sp_gxf2gxf"
  executable: "target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf
+++ b/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf
@@ -493,9 +493,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t

 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_sp_gxf2gxf"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:45Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:07:55Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/arriba/.config.vsh.yaml
+++ b/target/executable/arriba/.config.vsh.yaml
@@ -706,9 +706,9 @@ build_info:
  output: "target/executable/arriba"
  executable: "target/executable/arriba/arriba"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/arriba/arriba
+++ b/target/executable/arriba/arriba
@@ -754,9 +754,9 @@ RUN arriba -h | grep 'Version:' 2>&1 |  sed 's/Version:\s\(.*\)/arriba: "\1"/' >

 LABEL org.opencontainers.image.authors="Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component arriba"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:49Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:07:59Z"
 LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bcftools/bcftools_annotate/.config.vsh.yaml
+++ b/target/executable/bcftools/bcftools_annotate/.config.vsh.yaml
@@ -469,9 +469,9 @@ build_info:
  output: "target/executable/bcftools/bcftools_annotate"
  executable: "target/executable/bcftools/bcftools_annotate/bcftools_annotate"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bcftools/bcftools_annotate/bcftools_annotate
+++ b/target/executable/bcftools/bcftools_annotate/bcftools_annotate
@@ -650,9 +650,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_annotate"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:39Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:07:49Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bcftools/bcftools_concat/.config.vsh.yaml
+++ b/target/executable/bcftools/bcftools_concat/.config.vsh.yaml
@@ -335,9 +335,9 @@ build_info:
  output: "target/executable/bcftools/bcftools_concat"
  executable: "target/executable/bcftools/bcftools_concat/bcftools_concat"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bcftools/bcftools_concat/bcftools_concat
+++ b/target/executable/bcftools/bcftools_concat/bcftools_concat
@@ -566,9 +566,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_concat"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:39Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:07:49Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bcftools/bcftools_norm/.config.vsh.yaml
+++ b/target/executable/bcftools/bcftools_norm/.config.vsh.yaml
@@ -416,9 +416,9 @@ build_info:
  output: "target/executable/bcftools/bcftools_norm"
  executable: "target/executable/bcftools/bcftools_norm/bcftools_norm"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bcftools/bcftools_norm/bcftools_norm
+++ b/target/executable/bcftools/bcftools_norm/bcftools_norm
@@ -589,9 +589,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_norm"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:40Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:07:50Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bcftools/bcftools_sort/.config.vsh.yaml
+++ b/target/executable/bcftools/bcftools_sort/.config.vsh.yaml
@@ -185,9 +185,9 @@ build_info:
  output: "target/executable/bcftools/bcftools_sort"
  executable: "target/executable/bcftools/bcftools_sort/bcftools_sort"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bcftools/bcftools_sort/bcftools_sort
+++ b/target/executable/bcftools/bcftools_sort/bcftools_sort
@@ -483,9 +483,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_sort"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:38Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:07:48Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bcftools/bcftools_stats/.config.vsh.yaml
+++ b/target/executable/bcftools/bcftools_stats/.config.vsh.yaml
@@ -458,9 +458,9 @@ build_info:
  output: "target/executable/bcftools/bcftools_stats"
  executable: "target/executable/bcftools/bcftools_stats/bcftools_stats"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bcftools/bcftools_stats/bcftools_stats
+++ b/target/executable/bcftools/bcftools_stats/bcftools_stats
@@ -626,9 +626,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_stats"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:39Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:07:49Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bcl_convert/.config.vsh.yaml
+++ b/target/executable/bcl_convert/.config.vsh.yaml
@@ -418,9 +418,9 @@ build_info:
  output: "target/executable/bcl_convert"
  executable: "target/executable/bcl_convert/bcl_convert"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bcl_convert/bcl_convert
+++ b/target/executable/bcl_convert/bcl_convert
@@ -599,9 +599,9 @@ RUN echo "bcl-convert: \"$(bcl-convert -V 2>&1 >/dev/null | sed -n '/Version/ s/

 LABEL org.opencontainers.image.authors="Toni Verbeiren, Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component bcl_convert"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:48Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:07:58Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml
+++ b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml
@@ -274,9 +274,9 @@ build_info:
  output: "target/executable/bd_rhapsody/bd_rhapsody_make_reference"
  executable: "target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference
+++ b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference
@@ -554,9 +554,9 @@ RUN VERSION=$(ls -v /var/bd_rhapsody_cwl | grep '^v' | sed 's#v##' | tail -1)
 RUN echo "bdgenomics/rhapsody: \"$VERSION\"" > /var/software_versions.txt
 LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Weiwei Schultz"
 LABEL org.opencontainers.image.description="Companion container for running component bd_rhapsody bd_rhapsody_make_reference"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:52Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:08:02Z"
 LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1/Extra_Utilities/"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml
+++ b/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml
@@ -1115,9 +1115,9 @@ build_info:
  output: "target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis"
  executable: "target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/bd_rhapsody_sequence_analysis"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/bd_rhapsody_sequence_analysis
+++ b/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/bd_rhapsody_sequence_analysis
@@ -954,9 +954,9 @@ RUN VERSION=$(ls -v /var/bd_rhapsody_cwl | grep '^v' | sed 's#v##' | tail -1)
 RUN echo "bdgenomics/rhapsody: \"$VERSION\"" > /var/software_versions.txt
 LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Weiwei Schultz"
 LABEL org.opencontainers.image.description="Companion container for running component bd_rhapsody bd_rhapsody_sequence_analysis"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:52Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:08:01Z"
 LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml
@@ -187,9 +187,9 @@ build_info:
  output: "target/executable/bedtools/bedtools_bamtofastq"
  executable: "target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq
+++ b/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq
@@ -483,9 +483,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bamtofastq"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:31Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:07:41Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml
@@ -176,9 +176,9 @@ build_info:
  output: "target/executable/bedtools/bedtools_bed12tobed6"
  executable: "target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6
+++ b/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6
@@ -480,9 +480,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bed12tobed6"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:30Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:07:40Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml
@@ -214,9 +214,9 @@ build_info:
  output: "target/executable/bedtools/bedtools_bedtobam"
  executable: "target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam
+++ b/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam
@@ -496,9 +496,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bedtobam"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:32Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:07:42Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml
@@ -337,9 +337,9 @@ build_info:
  output: "target/executable/bedtools/bedtools_genomecov"
  executable: "target/executable/bedtools/bedtools_genomecov/bedtools_genomecov"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov
+++ b/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov
@@ -591,9 +591,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_genomecov"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:29Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:07:40Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 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
@@ -232,9 +232,9 @@ build_info:
  output: "target/executable/bedtools/bedtools_getfasta"
  executable: "target/executable/bedtools/bedtools_getfasta/bedtools_getfasta"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta
+++ b/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta
@@ -526,9 +526,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_getfasta"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:30Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:07:40Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml
@@ -273,9 +273,9 @@ build_info:
  output: "target/executable/bedtools/bedtools_groupby"
  executable: "target/executable/bedtools/bedtools_groupby/bedtools_groupby"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bedtools/bedtools_groupby/bedtools_groupby
+++ b/target/executable/bedtools/bedtools_groupby/bedtools_groupby
@@ -552,9 +552,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_groupby"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:31Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:07:42Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml
@@ -410,9 +410,9 @@ build_info:
  output: "target/executable/bedtools/bedtools_intersect"
  executable: "target/executable/bedtools/bedtools_intersect/bedtools_intersect"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bedtools/bedtools_intersect/bedtools_intersect
+++ b/target/executable/bedtools/bedtools_intersect/bedtools_intersect
@@ -633,9 +633,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_intersect"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:30Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:07:40Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_links/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_links/.config.vsh.yaml
@@ -210,9 +210,9 @@ build_info:
  output: "target/executable/bedtools/bedtools_links"
  executable: "target/executable/bedtools/bedtools_links/bedtools_links"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bedtools/bedtools_links/bedtools_links
+++ b/target/executable/bedtools/bedtools_links/bedtools_links
@@ -500,9 +500,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_links"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:31Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:07:41Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_merge/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_merge/.config.vsh.yaml
@@ -279,9 +279,9 @@ build_info:
  output: "target/executable/bedtools/bedtools_merge"
  executable: "target/executable/bedtools/bedtools_merge/bedtools_merge"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bedtools/bedtools_merge/bedtools_merge
+++ b/target/executable/bedtools/bedtools_merge/bedtools_merge
@@ -558,9 +558,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_merge"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:29Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:07:39Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_sort/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_sort/.config.vsh.yaml
@@ -222,9 +222,9 @@ build_info:
  output: "target/executable/bedtools/bedtools_sort"
  executable: "target/executable/bedtools/bedtools_sort/bedtools_sort"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bedtools/bedtools_sort/bedtools_sort
+++ b/target/executable/bedtools/bedtools_sort/bedtools_sort
@@ -509,9 +509,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_sort"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:32Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:07:42Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 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
@@ -158,9 +158,9 @@ build_info:
  output: "target/executable/busco/busco_download_datasets"
  executable: "target/executable/busco/busco_download_datasets/busco_download_datasets"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/busco/busco_download_datasets/busco_download_datasets
+++ b/target/executable/busco/busco_download_datasets/busco_download_datasets
@@ -475,9 +475,9 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version

 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component busco busco_download_datasets"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:43Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:07:53Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 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
@@ -145,9 +145,9 @@ build_info:
  output: "target/executable/busco/busco_list_datasets"
  executable: "target/executable/busco/busco_list_datasets/busco_list_datasets"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/busco/busco_list_datasets/busco_list_datasets
+++ b/target/executable/busco/busco_list_datasets/busco_list_datasets
@@ -465,9 +465,9 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version

 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component busco busco_list_datasets"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:43Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:07:53Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 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
@@ -423,9 +423,9 @@ build_info:
  output: "target/executable/busco/busco_run"
  executable: "target/executable/busco/busco_run/busco_run"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/busco/busco_run/busco_run
+++ b/target/executable/busco/busco_run/busco_run
@@ -632,9 +632,9 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version

 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component busco busco_run"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:43Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:07:53Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/cutadapt/.config.vsh.yaml
+++ b/target/executable/cutadapt/.config.vsh.yaml
@@ -251,7 +251,7 @@ argument_groups:
    direction: "input"
    multiple: false
    multiple_sep: ";"
-  - type: "boolean_false"
+  - type: "boolean_true"
    name: "--no_indels"
    description: "Allow only mismatches in alignments.\n"
    info: null
@@ -286,7 +286,7 @@ argument_groups:
    description: "Interpret IUPAC wildcards in reads.\n"
    info: null
    direction: "input"
-  - type: "boolean_false"
+  - type: "boolean_true"
    name: "--no_match_adapter_wildcards"
    description: "Do not interpret IUPAC wildcards in adapters.\n"
    info: null
@@ -740,9 +740,9 @@ build_info:
  output: "target/executable/cutadapt"
  executable: "target/executable/cutadapt/cutadapt"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/cutadapt/cutadapt
+++ b/target/executable/cutadapt/cutadapt
@@ -322,7 +322,7 @@ function ViashHelp {
  echo "        length of matching region. Default: 0.1 (10%)."
  echo ""
  echo "    --no_indels"
-  echo "        type: boolean_false"
+  echo "        type: boolean_true"
  echo "        Allow only mismatches in alignments."
  echo ""
  echo "    -n, --times"
@@ -341,7 +341,7 @@ function ViashHelp {
  echo "        Interpret IUPAC wildcards in reads."
  echo ""
  echo "    --no_match_adapter_wildcards"
-  echo "        type: boolean_false"
+  echo "        type: boolean_true"
  echo "        Do not interpret IUPAC wildcards in adapters."
  echo ""
  echo "    --action"
@@ -831,9 +831,9 @@ RUN cutadapt --version | sed 's/\(.*\)/cutadapt: "\1"/' > /var/software_versions

 LABEL org.opencontainers.image.authors="Toni Verbeiren"
 LABEL org.opencontainers.image.description="Companion container for running component cutadapt"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:51Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:08:00Z"
 LABEL org.opencontainers.image.source="https://github.com/marcelm/cutadapt"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
@@ -1269,7 +1269,7 @@ while [[ $# -gt 0 ]]; do
            ;;
        --no_indels)
            [ -n "$VIASH_PAR_NO_INDELS" ] && ViashError Bad arguments for option \'--no_indels\': \'$VIASH_PAR_NO_INDELS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
-            VIASH_PAR_NO_INDELS=false
+            VIASH_PAR_NO_INDELS=true
            shift 1
            ;;
        --times)
@@ -1313,7 +1313,7 @@ while [[ $# -gt 0 ]]; do
            ;;
        --no_match_adapter_wildcards)
            [ -n "$VIASH_PAR_NO_MATCH_ADAPTER_WILDCARDS" ] && ViashError Bad arguments for option \'--no_match_adapter_wildcards\': \'$VIASH_PAR_NO_MATCH_ADAPTER_WILDCARDS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
-            VIASH_PAR_NO_MATCH_ADAPTER_WILDCARDS=false
+            VIASH_PAR_NO_MATCH_ADAPTER_WILDCARDS=true
            shift 1
            ;;
        --action)
@@ -1910,13 +1910,13 @@ if [ -z ${VIASH_PAR_INTERLEAVED+x} ]; then
  VIASH_PAR_INTERLEAVED="false"
 fi
 if [ -z ${VIASH_PAR_NO_INDELS+x} ]; then
-  VIASH_PAR_NO_INDELS="true"
+  VIASH_PAR_NO_INDELS="false"
 fi
 if [ -z ${VIASH_PAR_MATCH_READ_WILDCARDS+x} ]; then
  VIASH_PAR_MATCH_READ_WILDCARDS="false"
 fi
 if [ -z ${VIASH_PAR_NO_MATCH_ADAPTER_WILDCARDS+x} ]; then
-  VIASH_PAR_NO_MATCH_ADAPTER_WILDCARDS="true"
+  VIASH_PAR_NO_MATCH_ADAPTER_WILDCARDS="false"
 fi
 if [ -z ${VIASH_PAR_REVCOMP+x} ]; then
  VIASH_PAR_REVCOMP="false"
@@ -2015,7 +2015,7 @@ if [[ -n "$VIASH_PAR_ERROR_RATE" ]]; then
 fi
 if [[ -n "$VIASH_PAR_NO_INDELS" ]]; then
  if ! [[ "$VIASH_PAR_NO_INDELS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
-    ViashError '--no_indels' has to be a boolean_false. Use "--help" to get more information on the parameters.
+    ViashError '--no_indels' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
 fi
@@ -2039,7 +2039,7 @@ if [[ -n "$VIASH_PAR_MATCH_READ_WILDCARDS" ]]; then
 fi
 if [[ -n "$VIASH_PAR_NO_MATCH_ADAPTER_WILDCARDS" ]]; then
  if ! [[ "$VIASH_PAR_NO_MATCH_ADAPTER_WILDCARDS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
-    ViashError '--no_match_adapter_wildcards' has to be a boolean_false. Use "--help" to get more information on the parameters.
+    ViashError '--no_match_adapter_wildcards' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
 fi
@@ -2588,9 +2588,9 @@ debug
 # Input arguments 
 ###########################################################
 echo ">> Parsing input arguments"
-[[ "\$par_no_indels" == "true" ]] && unset par_no_indels
+[[ "\$par_no_indels" == "false" ]] && unset par_no_indels
 [[ "\$par_match_read_wildcards" == "false" ]] && unset par_match_read_wildcards
-[[ "\$par_no_match_adapter_wildcards" == "true" ]] && unset par_no_match_adapter_wildcards
+[[ "\$par_no_match_adapter_wildcards" == "false" ]] && unset par_no_match_adapter_wildcards
 [[ "\$par_revcomp" == "false" ]] && unset par_revcomp

 input_args=\$(echo \\
--- a/target/executable/falco/.config.vsh.yaml
+++ b/target/executable/falco/.config.vsh.yaml
@@ -317,9 +317,9 @@ build_info:
  output: "target/executable/falco"
  executable: "target/executable/falco/falco"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/falco/falco
+++ b/target/executable/falco/falco
@@ -589,9 +589,9 @@ RUN echo "falco: \"$(falco -v | sed -n 's/^falco //p')\"" > /var/software_versio

 LABEL org.opencontainers.image.authors="Toni Verbeiren"
 LABEL org.opencontainers.image.description="Companion container for running component falco"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:51Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:08:01Z"
 LABEL org.opencontainers.image.source="https://github.com/smithlabcode/falco"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/fastp/.config.vsh.yaml
+++ b/target/executable/fastp/.config.vsh.yaml
@@ -1083,9 +1083,9 @@ build_info:
  output: "target/executable/fastp"
  executable: "target/executable/fastp/fastp"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/fastp/fastp
+++ b/target/executable/fastp/fastp
@@ -1028,9 +1028,9 @@ RUN fastp --version 2>&1 | sed 's# #: "#;s#$#"#' > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component fastp"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:48Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:07:57Z"
 LABEL org.opencontainers.image.source="https://github.com/OpenGene/fastp"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/fastqc/.config.vsh.yaml
+++ b/target/executable/fastqc/.config.vsh.yaml
@@ -340,9 +340,9 @@ build_info:
  output: "target/executable/fastqc"
  executable: "target/executable/fastqc/fastqc"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/fastqc/fastqc
+++ b/target/executable/fastqc/fastqc
@@ -601,9 +601,9 @@ 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="2024-10-03T12:50:37Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:07:47Z"
 LABEL org.opencontainers.image.source="https://github.com/s-andrews/FastQC"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/featurecounts/.config.vsh.yaml
+++ b/target/executable/featurecounts/.config.vsh.yaml
@@ -645,9 +645,9 @@ build_info:
  output: "target/executable/featurecounts"
  executable: "target/executable/featurecounts/featurecounts"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/featurecounts/featurecounts
+++ b/target/executable/featurecounts/featurecounts
@@ -754,9 +754,9 @@ RUN featureCounts -v 2>&1 | sed 's/featureCounts v\([0-9.]*\)/featureCounts: \1/

 LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
 LABEL org.opencontainers.image.description="Companion container for running component featurecounts"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:41Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:07:51Z"
 LABEL org.opencontainers.image.source="https://github.com/ShiLab-Bioinformatics/subread"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/fq_subsample/.config.vsh.yaml
+++ b/target/executable/fq_subsample/.config.vsh.yaml
@@ -190,9 +190,9 @@ build_info:
  output: "target/executable/fq_subsample"
  executable: "target/executable/fq_subsample/fq_subsample"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/fq_subsample/fq_subsample
+++ b/target/executable/fq_subsample/fq_subsample
@@ -493,9 +493,9 @@ mv target/release/fq /usr/local/bin/ && \
 cd / && rm -rf /fq

 LABEL org.opencontainers.image.description="Companion container for running component fq_subsample"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:37Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:07:47Z"
 LABEL org.opencontainers.image.source="https://github.com/stjude-rust-labs/fq"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/gffread/.config.vsh.yaml
+++ b/target/executable/gffread/.config.vsh.yaml
@@ -685,9 +685,9 @@ build_info:
  output: "target/executable/gffread"
  executable: "target/executable/gffread/gffread"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/gffread/gffread
+++ b/target/executable/gffread/gffread
@@ -807,9 +807,9 @@ RUN echo "gffread: \"$(gffread --version 2>&1)\"" > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component gffread"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:28Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:07:39Z"
 LABEL org.opencontainers.image.source="https://github.com/gpertea/gffread"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/kallisto/kallisto_index/.config.vsh.yaml
+++ b/target/executable/kallisto/kallisto_index/.config.vsh.yaml
@@ -218,9 +218,9 @@ build_info:
  output: "target/executable/kallisto/kallisto_index"
  executable: "target/executable/kallisto/kallisto_index/kallisto_index"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/kallisto/kallisto_index/kallisto_index
+++ b/target/executable/kallisto/kallisto_index/kallisto_index
@@ -506,9 +506,9 @@ tar -xzf kallisto_linux-v0.50.1.tar.gz && \
 mv kallisto/kallisto /usr/local/bin/

 LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_index"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:45Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:07:55Z"
 LABEL org.opencontainers.image.source="https://github.com/pachterlab/kallisto"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/kallisto/kallisto_quant/.config.vsh.yaml
+++ b/target/executable/kallisto/kallisto_quant/.config.vsh.yaml
@@ -234,9 +234,9 @@ build_info:
  output: "target/executable/kallisto/kallisto_quant"
  executable: "target/executable/kallisto/kallisto_quant/kallisto_quant"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/kallisto/kallisto_quant/kallisto_quant
+++ b/target/executable/kallisto/kallisto_quant/kallisto_quant
@@ -518,9 +518,9 @@ mv kallisto/kallisto /usr/local/bin/
 RUN echo "kallisto: $(kallisto version | sed 's/kallisto, version //')" > /var/software_versions.txt

 LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_quant"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:45Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:07:55Z"
 LABEL org.opencontainers.image.source="https://github.com/pachterlab/kallisto"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 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
@@ -507,9 +507,9 @@ build_info:
  output: "target/executable/lofreq/lofreq_call"
  executable: "target/executable/lofreq/lofreq_call/lofreq_call"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/lofreq/lofreq_call/lofreq_call
+++ b/target/executable/lofreq/lofreq_call/lofreq_call
@@ -656,9 +656,9 @@ echo "lofreq: $version" > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Kai Waldrant"
 LABEL org.opencontainers.image.description="Companion container for running component lofreq lofreq_call"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:41Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:07:50Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 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
@@ -215,9 +215,9 @@ build_info:
  output: "target/executable/lofreq/lofreq_indelqual"
  executable: "target/executable/lofreq/lofreq_indelqual/lofreq_indelqual"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual
+++ b/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual
@@ -501,9 +501,9 @@ echo "lofreq: $version" > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Kai Waldrant"
 LABEL org.opencontainers.image.description="Companion container for running component lofreq lofreq_indelqual"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:40Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:07:50Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/multiqc/.config.vsh.yaml
+++ b/target/executable/multiqc/.config.vsh.yaml
@@ -456,9 +456,9 @@ build_info:
  output: "target/executable/multiqc"
  executable: "target/executable/multiqc/multiqc"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/multiqc/multiqc
+++ b/target/executable/multiqc/multiqc
@@ -637,9 +637,9 @@ RUN multiqc --version | sed 's/multiqc, version\s\(.*\)/multiqc: "\1"/' > /var/s

 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component multiqc"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:51Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:08:00Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/pear/.config.vsh.yaml
+++ b/target/executable/pear/.config.vsh.yaml
@@ -398,9 +398,9 @@ build_info:
  output: "target/executable/pear"
  executable: "target/executable/pear/pear"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/pear/pear
+++ b/target/executable/pear/pear
@@ -597,9 +597,9 @@ echo "pear: $version" > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Kai Waldrant"
 LABEL org.opencontainers.image.description="Companion container for running component pear"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:32Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:07:43Z"
 LABEL org.opencontainers.image.source="https://github.com/tseemann/PEAR"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml
+++ b/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml
@@ -264,9 +264,9 @@ build_info:
  output: "target/executable/qualimap/qualimap_rnaseq"
  executable: "target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq
+++ b/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq
@@ -527,9 +527,9 @@ RUN echo QualiMap: $(qualimap 2>&1 | grep QualiMap | sed 's/^.*QualiMap//') > /v

 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component qualimap qualimap_rnaseq"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:36Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:07:46Z"
 LABEL org.opencontainers.image.source="https://bitbucket.org/kokonech/qualimap/commits/branch/master"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml
+++ b/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml
@@ -852,9 +852,9 @@ build_info:
  output: "target/executable/rsem/rsem_calculate_expression"
  executable: "target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression
+++ b/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression
@@ -991,9 +991,9 @@ echo "bowtie: `bowtie --version | grep -oP 'bowtie-align-s version \K\d+\.\d+\.\
 echo "HISAT2: `hisat2 --version | grep -oP 'hisat2-align-s version \K\d+\.\d+\.\d+'`" >> /var/software_versions.txt

 LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_calculate_expression"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:44Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:07:54Z"
 LABEL org.opencontainers.image.source="https://github.com/deweylab/RSEM"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml
+++ b/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml
@@ -416,9 +416,9 @@ build_info:
  output: "target/executable/rsem/rsem_prepare_reference"
  executable: "target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference
+++ b/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference
@@ -656,9 +656,9 @@ echo "HISAT2: `hisat2 --version | grep -oP 'hisat2-align-s version \K\d+\.\d+\.\

 LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
 LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_prepare_reference"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:44Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:07:54Z"
 LABEL org.opencontainers.image.source="https://github.com/deweylab/RSEM"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 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
@@ -277,9 +277,9 @@ build_info:
  output: "target/executable/salmon/salmon_index"
  executable: "target/executable/salmon/salmon_index/salmon_index"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/salmon/salmon_index/salmon_index
+++ b/target/executable/salmon/salmon_index/salmon_index
@@ -546,9 +546,9 @@ RUN salmon index -v 2>&1 | sed 's/salmon \([0-9.]*\)/salmon: \1/' > /var/softwar

 LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
 LABEL org.opencontainers.image.description="Companion container for running component salmon salmon_index"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:50Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:07:59Z"
 LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 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
@@ -1173,9 +1173,9 @@ build_info:
  output: "target/executable/salmon/salmon_quant"
  executable: "target/executable/salmon/salmon_quant/salmon_quant"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/salmon/salmon_quant/salmon_quant
+++ b/target/executable/salmon/salmon_quant/salmon_quant
@@ -1168,9 +1168,9 @@ RUN salmon index -v 2>&1 | sed 's/salmon \([0-9.]*\)/salmon: \1/' > /var/softwar

 LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
 LABEL org.opencontainers.image.description="Companion container for running component salmon salmon_quant"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:50Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:07:59Z"
 LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 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
@@ -264,9 +264,9 @@ build_info:
  output: "target/executable/samtools/samtools_collate"
  executable: "target/executable/samtools/samtools_collate/samtools_collate"
  viash_version: "0.9.0"
-  git_commit: "0a0edcacb5368517d249210022363bd9265f1bf5"
-  git_remote: "https://x-access-token:ghs_bIjTemwR1Wh9ikbQ1ucI3bX39xxlpm0HUaHb@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-8-g0a0edca"
+  git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
+  git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-9-gadd1252"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/samtools/samtools_collate/samtools_collate
+++ b/target/executable/samtools/samtools_collate/samtools_collate
@@ -519,9 +519,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_collate"
-LABEL org.opencontainers.image.created="2024-10-03T12:50:35Z"
+LABEL org.opencontainers.image.created="2024-10-07T09:07:45Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="0a0edcacb5368517d249210022363bd9265f1bf5"
+LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/Show More
+++ b/Show More