Build branch main with version main (aa43543)

Build pipeline: viash-hub.biobox.main-2k68h Source commit: aa43543e1f Source message: Rseqc innerdistance (#159) * initial commit dedup * Revert "initial commit dedup" This reverts commit 38f586bec0ac9e4312b016e29c3aa0bd53f292b2. * full component with two tests * fix default values * adjust argument names and container image --------- Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
2024-10-26 19:02:37 +00:00
parent 35f315e911
commit a7b0d33a32
366 changed files with 37009 additions and 780 deletions
--- a/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml
@@ -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: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 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
@@ -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="2024-10-26T13:11:21Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:10Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- 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: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 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="2024-10-26T13:11:20Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:08Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 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: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 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="2024-10-26T13:11:19Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:07Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 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: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 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="2024-10-26T13:11:21Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:09Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 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: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 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="2024-10-26T13:11:20Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:08Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 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: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 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="2024-10-26T13:11:19Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:07Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/agat/agat_sp_add_introns/.config.vsh.yaml
+++ b/target/executable/agat/agat_sp_add_introns/.config.vsh.yaml
@@ -186,9 +186,9 @@ build_info:
  output: "target/executable/agat/agat_sp_add_introns"
  executable: "target/executable/agat/agat_sp_add_introns/agat_sp_add_introns"
  viash_version: "0.9.0"
-  git_commit: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/agat/agat_sp_add_introns/agat_sp_add_introns
+++ b/target/executable/agat/agat_sp_add_introns/agat_sp_add_introns
@@ -479,9 +479,9 @@ 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_sp_add_introns"
-LABEL org.opencontainers.image.created="2024-10-26T13:11:20Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:09Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/agat/agat_sp_filter_feature_from_kill_list/.config.vsh.yaml
+++ b/target/executable/agat/agat_sp_filter_feature_from_kill_list/.config.vsh.yaml
@@ -0,0 +1,263 @@
+name: "agat_sp_filter_feature_from_kill_list"
+namespace: "agat"
+version: "main"
+authors:
+- name: "Leïla Paquay"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "leila@data-intuitive.com"
+      github: "Leila011"
+      linkedin: "leilapaquay"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Software Developer"
+argument_groups:
+- name: "Inputs"
+  arguments:
+  - type: "file"
+    name: "--gff"
+    alternatives:
+    - "-f"
+    - "--ref"
+    - "--reffile"
+    description: "Input GFF3 file that will be read."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--kill_list"
+    alternatives:
+    - "--kl"
+    description: "Text file containing the kill list. One value per line."
+    info: null
+    example:
+    - "kill_list.txt"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    alternatives:
+    - "-o"
+    - "--out"
+    description: "Path to the output GFF file that contains filtered features. \n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Arguments"
+  arguments:
+  - type: "string"
+    name: "--type"
+    alternatives:
+    - "-p"
+    - "-l"
+    description: "Primary tag option, case insensitive, list. Allow to specify the\
+      \ feature types that \nwill be handled. \n\nYou can specify a specific feature\
+      \ by giving its primary tag name (column 3) as: \n\n  * cds\n  * Gene\n  * mRNA\n\
+      \  \nYou can specify directly all the feature of a particular\nlevel: \n\n \
+      \ * level2=mRNA,ncRNA,tRNA,etc \n  * level3=CDS,exon,UTR,etc. \n\nBy default\
+      \ all features are taken into account. Fill the option with the value \"all\"\
+      \ will \nhave the same behaviour.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+  - type: "string"
+    name: "--attribute"
+    alternatives:
+    - "-a"
+    description: "Attribute tag to specify the attribute to analyse. Case sensitive.\
+      \ Default: ID\n"
+    info: null
+    example:
+    - "ID"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--config"
+    alternatives:
+    - "-c"
+    description: "AGAT config file. By default AGAT takes the original agat_config.yaml\
+      \ shipped with AGAT.\nThe `--config` option gives you the possibility to use\
+      \ your own AGAT config file (located \nelsewhere or named differently).\n"
+    info: null
+    example:
+    - "custom_agat_config.yaml"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--verbose"
+    alternatives:
+    - "-v"
+    description: "Verbose option for debugging purpose."
+    info: null
+    direction: "input"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Remove features based on a kill list. The default behaviour is to look\
+  \ at the features's ID. \nIf the feature has an ID (case insensitive) listed among\
+  \ the kill list it will be removed.\nRemoving a level1 or level2 feature will automatically\
+  \ remove all linked subfeatures, and \nremoving all children of a feature will automatically\
+  \ remove this feature too.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test_data"
+info: null
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "gene annotations"
+- "filtering"
+- "gff"
+license: "GPL-3.0"
+references:
+  doi:
+  - "10.5281/zenodo.3552717"
+links:
+  repository: "https://github.com/NBISweden/AGAT"
+  homepage: "https://github.com/NBISweden/AGAT"
+  documentation: "https://agat.readthedocs.io/en/latest/tools/agat_sp_filter_feature_from_kill_list.html"
+  issue_tracker: "https://github.com/NBISweden/AGAT/issues"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$id"
+  auto:
+    simplifyInput: true
+    simplifyOutput: false
+    transcript: false
+    publish: false
+  config:
+    labels:
+      mem1gb: "memory = 1000000000.B"
+      mem2gb: "memory = 2000000000.B"
+      mem5gb: "memory = 5000000000.B"
+      mem10gb: "memory = 10000000000.B"
+      mem20gb: "memory = 20000000000.B"
+      mem50gb: "memory = 50000000000.B"
+      mem100gb: "memory = 100000000000.B"
+      mem200gb: "memory = 200000000000.B"
+      mem500gb: "memory = 500000000000.B"
+      mem1tb: "memory = 1000000000000.B"
+      mem2tb: "memory = 2000000000000.B"
+      mem5tb: "memory = 5000000000000.B"
+      mem10tb: "memory = 10000000000000.B"
+      mem20tb: "memory = 20000000000000.B"
+      mem50tb: "memory = 50000000000000.B"
+      mem100tb: "memory = 100000000000000.B"
+      mem200tb: "memory = 200000000000000.B"
+      mem500tb: "memory = 500000000000000.B"
+      mem1gib: "memory = 1073741824.B"
+      mem2gib: "memory = 2147483648.B"
+      mem4gib: "memory = 4294967296.B"
+      mem8gib: "memory = 8589934592.B"
+      mem16gib: "memory = 17179869184.B"
+      mem32gib: "memory = 34359738368.B"
+      mem64gib: "memory = 68719476736.B"
+      mem128gib: "memory = 137438953472.B"
+      mem256gib: "memory = 274877906944.B"
+      mem512gib: "memory = 549755813888.B"
+      mem1tib: "memory = 1099511627776.B"
+      mem2tib: "memory = 2199023255552.B"
+      mem4tib: "memory = 4398046511104.B"
+      mem8tib: "memory = 8796093022208.B"
+      mem16tib: "memory = 17592186044416.B"
+      mem32tib: "memory = 35184372088832.B"
+      mem64tib: "memory = 70368744177664.B"
+      mem128tib: "memory = 140737488355328.B"
+      mem256tib: "memory = 281474976710656.B"
+      mem512tib: "memory = 562949953421312.B"
+      cpu1: "cpus = 1"
+      cpu2: "cpus = 2"
+      cpu5: "cpus = 5"
+      cpu10: "cpus = 10"
+      cpu20: "cpus = 20"
+      cpu50: "cpus = 50"
+      cpu100: "cpus = 100"
+      cpu200: "cpus = 200"
+      cpu500: "cpus = 500"
+      cpu1000: "cpus = 1000"
+  debug: false
+  container: "docker"
+engines:
+- type: "docker"
+  id: "docker"
+  image: "quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0"
+  target_registry: "images.viash-hub.com"
+  target_tag: "main"
+  namespace_separator: "/"
+  setup:
+  - type: "docker"
+    run:
+    - "agat --version | sed 's/AGAT\\s\\(.*\\)/agat: \"\\1\"/' > /var/software_versions.txt\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/agat/agat_sp_filter_feature_from_kill_list/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/agat/agat_sp_filter_feature_from_kill_list"
+  executable: "target/executable/agat/agat_sp_filter_feature_from_kill_list/agat_sp_filter_feature_from_kill_list"
+  viash_version: "0.9.0"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
+package_config:
+  name: "biobox"
+  version: "main"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.0"
+  source: "src"
+  target: "target"
+  config_mods:
+  - ".requirements.commands := ['ps']\n"
+  - ".engines += { type: \"native\" }"
+  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
+  - ".engines[.type == 'docker'].target_tag := 'main'"
+  keywords:
+  - "bioinformatics"
+  - "modules"
+  - "sequencing"
+  license: "MIT"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/viash-hub/biobox"
+    issue_tracker: "https://github.com/viash-hub/biobox/issues"
--- a/target/executable/agat/agat_sp_filter_feature_from_kill_list/agat_sp_filter_feature_from_kill_list
+++ b/target/executable/agat/agat_sp_filter_feature_from_kill_list/agat_sp_filter_feature_from_kill_list
--- a/target/executable/agat/agat_sp_merge_annotations/.config.vsh.yaml
+++ b/target/executable/agat/agat_sp_merge_annotations/.config.vsh.yaml
@@ -0,0 +1,211 @@
+name: "agat_sp_merge_annotations"
+namespace: "agat"
+version: "main"
+authors:
+- name: "Leïla Paquay"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "leila@data-intuitive.com"
+      github: "Leila011"
+      linkedin: "leilapaquay"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Software Developer"
+argument_groups:
+- name: "Inputs"
+  arguments:
+  - type: "file"
+    name: "--gff"
+    alternatives:
+    - "-f"
+    description: "Input GTF/GFF file(s).\n"
+    info: null
+    example:
+    - "input1.gff;input2.gff"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    alternatives:
+    - "-o"
+    - "--out"
+    description: "Output gff3 file where the gene incriminated will be writen."
+    info: null
+    example:
+    - "output.gff"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Arguments"
+  arguments:
+  - type: "file"
+    name: "--config"
+    alternatives:
+    - "-c"
+    description: "AGAT config file. By default AGAT takes the original agat_config.yaml\
+      \ shipped with AGAT. \nThe `--config` option gives you the possibility to use\
+      \ your own AGAT config file (located\nelsewhere or named differently).\n"
+    info: null
+    example:
+    - "custom_agat_config.yaml"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Merge different gff annotation files into one. It uses the AGAT parser\
+  \ that takes care of\nduplicated names and fixes other oddities met in those files.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test_data"
+info: null
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "gene annotations"
+- "merge"
+- "gff"
+license: "GPL-3.0"
+references:
+  doi:
+  - "10.5281/zenodo.3552717"
+links:
+  repository: "https://github.com/NBISweden/AGAT"
+  homepage: "https://github.com/NBISweden/AGAT"
+  documentation: "https://agat.readthedocs.io/en/latest/tools/agat_sp_merge_annotations.html"
+  issue_tracker: "https://github.com/NBISweden/AGAT/issues"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$id"
+  auto:
+    simplifyInput: true
+    simplifyOutput: false
+    transcript: false
+    publish: false
+  config:
+    labels:
+      mem1gb: "memory = 1000000000.B"
+      mem2gb: "memory = 2000000000.B"
+      mem5gb: "memory = 5000000000.B"
+      mem10gb: "memory = 10000000000.B"
+      mem20gb: "memory = 20000000000.B"
+      mem50gb: "memory = 50000000000.B"
+      mem100gb: "memory = 100000000000.B"
+      mem200gb: "memory = 200000000000.B"
+      mem500gb: "memory = 500000000000.B"
+      mem1tb: "memory = 1000000000000.B"
+      mem2tb: "memory = 2000000000000.B"
+      mem5tb: "memory = 5000000000000.B"
+      mem10tb: "memory = 10000000000000.B"
+      mem20tb: "memory = 20000000000000.B"
+      mem50tb: "memory = 50000000000000.B"
+      mem100tb: "memory = 100000000000000.B"
+      mem200tb: "memory = 200000000000000.B"
+      mem500tb: "memory = 500000000000000.B"
+      mem1gib: "memory = 1073741824.B"
+      mem2gib: "memory = 2147483648.B"
+      mem4gib: "memory = 4294967296.B"
+      mem8gib: "memory = 8589934592.B"
+      mem16gib: "memory = 17179869184.B"
+      mem32gib: "memory = 34359738368.B"
+      mem64gib: "memory = 68719476736.B"
+      mem128gib: "memory = 137438953472.B"
+      mem256gib: "memory = 274877906944.B"
+      mem512gib: "memory = 549755813888.B"
+      mem1tib: "memory = 1099511627776.B"
+      mem2tib: "memory = 2199023255552.B"
+      mem4tib: "memory = 4398046511104.B"
+      mem8tib: "memory = 8796093022208.B"
+      mem16tib: "memory = 17592186044416.B"
+      mem32tib: "memory = 35184372088832.B"
+      mem64tib: "memory = 70368744177664.B"
+      mem128tib: "memory = 140737488355328.B"
+      mem256tib: "memory = 281474976710656.B"
+      mem512tib: "memory = 562949953421312.B"
+      cpu1: "cpus = 1"
+      cpu2: "cpus = 2"
+      cpu5: "cpus = 5"
+      cpu10: "cpus = 10"
+      cpu20: "cpus = 20"
+      cpu50: "cpus = 50"
+      cpu100: "cpus = 100"
+      cpu200: "cpus = 200"
+      cpu500: "cpus = 500"
+      cpu1000: "cpus = 1000"
+  debug: false
+  container: "docker"
+engines:
+- type: "docker"
+  id: "docker"
+  image: "quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0"
+  target_registry: "images.viash-hub.com"
+  target_tag: "main"
+  namespace_separator: "/"
+  setup:
+  - type: "docker"
+    run:
+    - "agat --version | sed 's/AGAT\\s\\(.*\\)/agat: \"\\1\"/' > /var/software_versions.txt\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/agat/agat_sp_merge_annotations/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/agat/agat_sp_merge_annotations"
+  executable: "target/executable/agat/agat_sp_merge_annotations/agat_sp_merge_annotations"
+  viash_version: "0.9.0"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
+package_config:
+  name: "biobox"
+  version: "main"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.0"
+  source: "src"
+  target: "target"
+  config_mods:
+  - ".requirements.commands := ['ps']\n"
+  - ".engines += { type: \"native\" }"
+  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
+  - ".engines[.type == 'docker'].target_tag := 'main'"
+  keywords:
+  - "bioinformatics"
+  - "modules"
+  - "sequencing"
+  license: "MIT"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/viash-hub/biobox"
+    issue_tracker: "https://github.com/viash-hub/biobox/issues"
--- a/target/executable/agat/agat_sp_merge_annotations/agat_sp_merge_annotations
+++ b/target/executable/agat/agat_sp_merge_annotations/agat_sp_merge_annotations
--- a/target/executable/agat/agat_sp_statistics/.config.vsh.yaml
+++ b/target/executable/agat/agat_sp_statistics/.config.vsh.yaml
@@ -231,9 +231,9 @@ build_info:
  output: "target/executable/agat/agat_sp_statistics"
  executable: "target/executable/agat/agat_sp_statistics/agat_sp_statistics"
  viash_version: "0.9.0"
-  git_commit: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/agat/agat_sp_statistics/agat_sp_statistics
+++ b/target/executable/agat/agat_sp_statistics/agat_sp_statistics
@@ -507,9 +507,9 @@ RUN agat --version | sed 's/.*v\.//; s/\s.*//' | sed 's/^/AGAT: /' > /var/softwa

 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_sp_statistics"
-LABEL org.opencontainers.image.created="2024-10-26T13:11:20Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:09Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 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: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 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="2024-10-26T13:11:21Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:10Z"
 LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bbmap/bbmap_bbsplit/.config.vsh.yaml
+++ b/target/executable/bbmap/bbmap_bbsplit/.config.vsh.yaml
@@ -359,9 +359,9 @@ build_info:
  output: "target/executable/bbmap/bbmap_bbsplit"
  executable: "target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit"
  viash_version: "0.9.0"
-  git_commit: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit
+++ b/target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit
@@ -600,9 +600,9 @@ cp -r bbmap/* /usr/local/bin
 RUN bbsplit.sh --version 2>&1 | awk '/BBMap version/{print "BBMAP:", $NF}' > /var/software_versions.txt

 LABEL org.opencontainers.image.description="Companion container for running component bbmap bbmap_bbsplit"
-LABEL org.opencontainers.image.created="2024-10-26T13:11:24Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:12Z"
 LABEL org.opencontainers.image.source="https://github.com/BioInfoTools/BBMap/blob/master/sh/bbsplit.sh"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 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: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 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="2024-10-26T13:11:12Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:00Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 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: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 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="2024-10-26T13:11:13Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:01Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 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: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 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="2024-10-26T13:11:14Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:02Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 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: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 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="2024-10-26T13:11:14Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:02Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 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: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 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="2024-10-26T13:11:13Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:01Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 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: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 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="2024-10-26T13:11:19Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:07Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 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: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 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="2024-10-26T13:11:16Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:03Z"
 LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1/Extra_Utilities/"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 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: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 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="2024-10-26T13:11:16Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:03Z"
 LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_bamtobed/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_bamtobed/.config.vsh.yaml
@@ -0,0 +1,262 @@
+name: "bedtools_bamtobed"
+namespace: "bedtools"
+version: "main"
+authors:
+- name: "Theodoro Gasperin Terra Camargo"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "theodorogtc@gmail.com"
+      github: "tgaspe"
+      linkedin: "theodoro-gasperin-terra-camargo"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Bioinformatician"
+argument_groups:
+- name: "Inputs"
+  arguments:
+  - type: "file"
+    name: "--input"
+    alternatives:
+    - "-i"
+    description: "Input BAM file."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    alternatives:
+    - "-o"
+    description: "Output BED file."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Options"
+  arguments:
+  - type: "boolean_true"
+    name: "--bedpe"
+    description: "Write BEDPE format. Requires BAM to be grouped or sorted by query.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--mate1"
+    description: "When writing BEDPE (-bedpe) format, always report mate one as the\
+      \ first BEDPE \"block\".\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--bed12"
+    description: "Write \"blocked\" BED format (aka \"BED12\"). Forces -split.\nSee\
+      \ http://genome-test.cse.ucsc.edu/FAQ/FAQformat#format1\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--split"
+    description: "Report \"split\" BAM alignments as separate BED entries.\nSplits\
+      \ only on N CIGAR operations.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--splitD"
+    description: "Split alignments based on N and D CIGAR operators.\nForces -split.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--edit_distance"
+    alternatives:
+    - "-ed"
+    description: "Use BAM edit distance (NM tag) for BED score.\n- Default for BED\
+      \ is to use mapping quality.\n- Default for BEDPE is to use the minimum of\n\
+      \  the two mapping qualities for the pair.\n- When -ed is used with -bedpe,\
+      \ the total edit\n  distance from the two mates is reported.\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--tag"
+    description: "Use other NUMERIC BAM alignment tag for BED score.\nDefault for\
+      \ BED is to use mapping quality. Disallowed with BEDPE output.\n"
+    info: null
+    example:
+    - "SM"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--color"
+    description: "An R,G,B string for the color used with BED12 format.\nDefault is\
+      \ (255,0,0).\n"
+    info: null
+    example:
+    - "250,250,250"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--cigar"
+    description: "Add the CIGAR string to the BED entry as a 7th column.\n"
+    info: null
+    direction: "input"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Converts BAM alignments to BED6 or BEDPE format."
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test_data"
+info: null
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "Converts"
+- "BAM"
+- "BED"
+- "BED6"
+- "BEDPE"
+license: "MIT"
+references:
+  doi:
+  - "10.1093/bioinformatics/btq033"
+links:
+  repository: "https://github.com/arq5x/bedtools2"
+  homepage: "https://bedtools.readthedocs.io/en/latest/#"
+  documentation: "https://bedtools.readthedocs.io/en/latest/content/tools/bamtobed.html"
+  issue_tracker: "https://github.com/arq5x/bedtools2/issues"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$id"
+  auto:
+    simplifyInput: true
+    simplifyOutput: false
+    transcript: false
+    publish: false
+  config:
+    labels:
+      mem1gb: "memory = 1000000000.B"
+      mem2gb: "memory = 2000000000.B"
+      mem5gb: "memory = 5000000000.B"
+      mem10gb: "memory = 10000000000.B"
+      mem20gb: "memory = 20000000000.B"
+      mem50gb: "memory = 50000000000.B"
+      mem100gb: "memory = 100000000000.B"
+      mem200gb: "memory = 200000000000.B"
+      mem500gb: "memory = 500000000000.B"
+      mem1tb: "memory = 1000000000000.B"
+      mem2tb: "memory = 2000000000000.B"
+      mem5tb: "memory = 5000000000000.B"
+      mem10tb: "memory = 10000000000000.B"
+      mem20tb: "memory = 20000000000000.B"
+      mem50tb: "memory = 50000000000000.B"
+      mem100tb: "memory = 100000000000000.B"
+      mem200tb: "memory = 200000000000000.B"
+      mem500tb: "memory = 500000000000000.B"
+      mem1gib: "memory = 1073741824.B"
+      mem2gib: "memory = 2147483648.B"
+      mem4gib: "memory = 4294967296.B"
+      mem8gib: "memory = 8589934592.B"
+      mem16gib: "memory = 17179869184.B"
+      mem32gib: "memory = 34359738368.B"
+      mem64gib: "memory = 68719476736.B"
+      mem128gib: "memory = 137438953472.B"
+      mem256gib: "memory = 274877906944.B"
+      mem512gib: "memory = 549755813888.B"
+      mem1tib: "memory = 1099511627776.B"
+      mem2tib: "memory = 2199023255552.B"
+      mem4tib: "memory = 4398046511104.B"
+      mem8tib: "memory = 8796093022208.B"
+      mem16tib: "memory = 17592186044416.B"
+      mem32tib: "memory = 35184372088832.B"
+      mem64tib: "memory = 70368744177664.B"
+      mem128tib: "memory = 140737488355328.B"
+      mem256tib: "memory = 281474976710656.B"
+      mem512tib: "memory = 562949953421312.B"
+      cpu1: "cpus = 1"
+      cpu2: "cpus = 2"
+      cpu5: "cpus = 5"
+      cpu10: "cpus = 10"
+      cpu20: "cpus = 20"
+      cpu50: "cpus = 50"
+      cpu100: "cpus = 100"
+      cpu200: "cpus = 200"
+      cpu500: "cpus = 500"
+      cpu1000: "cpus = 1000"
+  debug: false
+  container: "docker"
+engines:
+- type: "docker"
+  id: "docker"
+  image: "debian:stable-slim"
+  target_registry: "images.viash-hub.com"
+  target_tag: "main"
+  namespace_separator: "/"
+  setup:
+  - type: "apt"
+    packages:
+    - "bedtools"
+    - "procps"
+    interactive: false
+  - type: "docker"
+    run:
+    - "echo \"bedtools: \\\"$(bedtools --version | sed -n 's/^bedtools //p')\\\"\"\
+      \ > /var/software_versions.txt\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/bedtools/bedtools_bamtobed/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/bedtools/bedtools_bamtobed"
+  executable: "target/executable/bedtools/bedtools_bamtobed/bedtools_bamtobed"
+  viash_version: "0.9.0"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
+package_config:
+  name: "biobox"
+  version: "main"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.0"
+  source: "src"
+  target: "target"
+  config_mods:
+  - ".requirements.commands := ['ps']\n"
+  - ".engines += { type: \"native\" }"
+  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
+  - ".engines[.type == 'docker'].target_tag := 'main'"
+  keywords:
+  - "bioinformatics"
+  - "modules"
+  - "sequencing"
+  license: "MIT"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/viash-hub/biobox"
+    issue_tracker: "https://github.com/viash-hub/biobox/issues"
--- a/target/executable/bedtools/bedtools_bamtobed/bedtools_bamtobed
+++ b/target/executable/bedtools/bedtools_bamtobed/bedtools_bamtobed
--- 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: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 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="2024-10-26T13:11:20Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:07Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 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: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 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="2024-10-26T13:11:21Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:09Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 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: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 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="2024-10-26T13:11:22Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:10Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 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: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 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="2024-10-26T13:11:20Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:08Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 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: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 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="2024-10-26T13:11:22Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:10Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 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: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 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="2024-10-26T13:11:21Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:09Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 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: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 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="2024-10-26T13:11:19Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:07Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 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: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 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="2024-10-26T13:11:20Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:08Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 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: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 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="2024-10-26T13:11:21Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:09Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 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: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 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="2024-10-26T13:11:19Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:07Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 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: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 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="2024-10-26T13:11:18Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:06Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 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: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 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="2024-10-26T13:11:18Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:06Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 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: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 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="2024-10-26T13:11:18Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:06Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/cutadapt/.config.vsh.yaml
+++ b/target/executable/cutadapt/.config.vsh.yaml
@@ -740,9 +740,9 @@ build_info:
  output: "target/executable/cutadapt"
  executable: "target/executable/cutadapt/cutadapt"
  viash_version: "0.9.0"
-  git_commit: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/cutadapt/cutadapt
+++ b/target/executable/cutadapt/cutadapt
@@ -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="2024-10-26T13:11:09Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:43:58Z"
 LABEL org.opencontainers.image.source="https://github.com/marcelm/cutadapt"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- 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: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 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="2024-10-26T13:11:11Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:00Z"
 LABEL org.opencontainers.image.source="https://github.com/smithlabcode/falco"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 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: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 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="2024-10-26T13:11:15Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:03Z"
 LABEL org.opencontainers.image.source="https://github.com/OpenGene/fastp"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 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: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 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="2024-10-26T13:11:16Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:04Z"
 LABEL org.opencontainers.image.source="https://github.com/s-andrews/FastQC"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 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: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 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="2024-10-26T13:11:12Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:00Z"
 LABEL org.opencontainers.image.source="https://github.com/ShiLab-Bioinformatics/subread"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 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: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 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="2024-10-26T13:11:12Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:00Z"
 LABEL org.opencontainers.image.source="https://github.com/stjude-rust-labs/fq"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 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: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 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="2024-10-26T13:11:16Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:04Z"
 LABEL org.opencontainers.image.source="https://github.com/gpertea/gffread"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 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: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 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="2024-10-26T13:11:22Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:10Z"
 LABEL org.opencontainers.image.source="https://github.com/pachterlab/kallisto"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 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: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 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="2024-10-26T13:11:22Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:11Z"
 LABEL org.opencontainers.image.source="https://github.com/pachterlab/kallisto"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 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: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 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="2024-10-26T13:11:23Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:11Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 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: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 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="2024-10-26T13:11:23Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:12Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 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: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 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="2024-10-26T13:11:18Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:05Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/nanoplot/.config.vsh.yaml
+++ b/target/executable/nanoplot/.config.vsh.yaml
@@ -492,9 +492,9 @@ build_info:
  output: "target/executable/nanoplot"
  executable: "target/executable/nanoplot/nanoplot"
  viash_version: "0.9.0"
-  git_commit: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/nanoplot/nanoplot
+++ b/target/executable/nanoplot/nanoplot
@@ -661,9 +661,9 @@ RUN version=$(NanoPlot --version) && \
 echo "$version" > /var/software_versions.txt

 LABEL org.opencontainers.image.description="Companion container for running component nanoplot"
-LABEL org.opencontainers.image.created="2024-10-26T13:11:18Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:05Z"
 LABEL org.opencontainers.image.source="https://github.com/wdecoster/NanoPlot"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 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: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 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="2024-10-26T13:11:08Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:43:57Z"
 LABEL org.opencontainers.image.source="https://github.com/tseemann/PEAR"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 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: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 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="2024-10-26T13:11:13Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:44:00Z"
 LABEL org.opencontainers.image.source="https://bitbucket.org/kokonech/qualimap/commits/branch/master"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 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: "52f44f5049606ac655154cf54ed53fa76b49896f"
-  git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-14-g52f44f5"
+  git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
+  git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-20-gaa43543"
 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="2024-10-26T13:11:11Z"
+LABEL org.opencontainers.image.created="2024-10-26T18:43:59Z"
 LABEL org.opencontainers.image.source="https://github.com/deweylab/RSEM"
-LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
+LABEL org.opencontainers.image.revision="aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
 LABEL org.opencontainers.image.version="main"

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