Build branch main with version main (8f525f5)

Build pipeline: viash-hub.biobox.main-x27rr Source commit: 8f525f5e40 Source message: Bedtools_Intersect (#94) * Initial Commit * Update config.vsh.yaml * creating templates * Update config.vsh.yaml * Update script.sh * Added output * Update config.vsh.yaml * Update test.sh * Update test.sh * More tests * small changes * update - change some var names - debugged - added more test * Update CHANGELOG.md * Update * Update help.txt
2024-07-31 19:42:45 +00:00
parent 02c1c9ebea
commit 2f26c0291a
151 changed files with 8077 additions and 175 deletions
--- a/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml
@@ -228,7 +228,7 @@ 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-RC6"
-  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
+  git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf
+++ b/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf
@@ -518,9 +518,9 @@ 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="2024-07-29T07:58:07Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:23:05Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
+LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/arriba/.config.vsh.yaml
+++ b/target/executable/arriba/.config.vsh.yaml
@@ -706,7 +706,7 @@ build_info:
  output: "target/executable/arriba"
  executable: "target/executable/arriba/arriba"
  viash_version: "0.9.0-RC6"
-  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
+  git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/arriba/arriba
+++ b/target/executable/arriba/arriba
@@ -753,9 +753,9 @@ 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="2024-07-29T07:58:02Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:22:58Z"
 LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba"
-LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
+LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bcl_convert/.config.vsh.yaml
+++ b/target/executable/bcl_convert/.config.vsh.yaml
@@ -418,7 +418,7 @@ build_info:
  output: "target/executable/bcl_convert"
  executable: "target/executable/bcl_convert/bcl_convert"
  viash_version: "0.9.0-RC6"
-  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
+  git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/bcl_convert/bcl_convert
+++ b/target/executable/bcl_convert/bcl_convert
@@ -598,9 +598,9 @@ 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="2024-07-29T07:58:02Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:22:59Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
+LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
 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
@@ -270,7 +270,7 @@ 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-RC6"
-  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
+  git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- 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
@@ -548,9 +548,9 @@ RUN echo "bdgenomics/rhapsody: 2.2.1" > /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="2024-07-29T07:58:08Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:23:06Z"
 LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1/Extra_Utilities/"
-LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
+LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
 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
@@ -232,7 +232,7 @@ build_info:
  output: "target/executable/bedtools/bedtools_getfasta"
  executable: "target/executable/bedtools/bedtools_getfasta/bedtools_getfasta"
  viash_version: "0.9.0-RC6"
-  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
+  git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta
+++ b/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta
@@ -525,9 +525,9 @@ 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="2024-07-29T07:58:04Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:23:01Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
+LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
 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
@@ -0,0 +1,436 @@
+name: "bedtools_intersect"
+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_a"
+    alternatives:
+    - "-a"
+    description: "The input file (BED/GFF/VCF/BAM) to be used as the -a file.\n"
+    info: null
+    example:
+    - "input_a.bed"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--input_b"
+    alternatives:
+    - "-b"
+    description: "The input file(s) (BED/GFF/VCF/BAM) to be used as the -b file(s).\n"
+    info: null
+    example:
+    - "input_b.bed"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    description: "The output BED file. \n"
+    info: null
+    example:
+    - "output.bed"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Options"
+  arguments:
+  - type: "boolean_true"
+    name: "--write_a"
+    alternatives:
+    - "-wa"
+    description: "Write the original A entry for each overlap."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--write_b"
+    alternatives:
+    - "-wb"
+    description: "Write the original B entry for each overlap. \nUseful for knowing\
+      \ _what_ A overlaps. Restricted by -f and -r.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--left_outer_join"
+    alternatives:
+    - "-loj"
+    description: "Perform a \"left outer join\". That is, for each feature in A report\
+      \ each overlap with B. \nIf no overlaps are found, report a NULL feature for\
+      \ B.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--write_overlap"
+    alternatives:
+    - "-wo"
+    description: "Write the original A and B entries plus the number of base pairs\
+      \ of overlap between the two features.\n- Overlaps restricted by -f and -r.\
+      \ \n  Only A features with overlap are reported.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--write_overlap_plus"
+    alternatives:
+    - "-wao"
+    description: "Write the original A and B entries plus the number of base pairs\
+      \ of overlap between the two features.\n- Overlaps restricted by -f and -r.\
+      \ \n  However, A features w/o overlap are also reported with a NULL B feature\
+      \ and overlap = 0.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--report_A_if_no_overlap"
+    alternatives:
+    - "-u"
+    description: "Write the original A entry _if_ no overlap is found. \n- In other\
+      \ words, just report the fact >=1 hit was found.\n- Overlaps restricted by -f\
+      \ and -r. \n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--number_of_overlaps_A"
+    alternatives:
+    - "-c"
+    description: "For each entry in A, report the number of overlaps with B.\n- Reports\
+      \ 0 for A entries that have no overlap with B.\n- Overlaps restricted by -f\
+      \ and -r.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--report_no_overlaps_A"
+    alternatives:
+    - "-v"
+    description: "Only report those entries in A that have _no overlaps_ with B.\n\
+      - Similar to \"grep -v\" (an homage).\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--uncompressed_bam"
+    alternatives:
+    - "-ubam"
+    description: "Write uncompressed BAM output. Default writes compressed BAM."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--same_strand"
+    alternatives:
+    - "-s"
+    description: "Require same strandedness.  That is, only report hits in B.\nthat\
+      \ overlap A on the _same_ strand.\n- By default, overlaps are reported without\
+      \ respect to strand.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--opposite_strand"
+    alternatives:
+    - "-S"
+    description: "Require different strandedness.  That is, only report hits in B\n\
+      that overlap A on the _opposite_ strand.\n- By default, overlaps are reported\
+      \ without respect to strand.\n"
+    info: null
+    direction: "input"
+  - type: "double"
+    name: "--min_overlap_A"
+    alternatives:
+    - "-f"
+    description: "Minimum overlap required as a fraction of A.\n- Default is 1E-9\
+      \ (i.e., 1bp).\n- FLOAT (e.g. 0.50)\n"
+    info: null
+    example:
+    - 0.5
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "double"
+    name: "--min_overlap_B"
+    alternatives:
+    - "-F"
+    description: "Minimum overlap required as a fraction of B.\n- Default is 1E-9\
+      \ (i.e., 1bp).\n- FLOAT (e.g. 0.50)\n"
+    info: null
+    example:
+    - 0.5
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--reciprocal_overlap"
+    alternatives:
+    - "-r"
+    description: "Require that the fraction overlap be reciprocal for A AND B.\n-\
+      \ In other words, if -f is 0.90 and -r is used, this requires\nthat B overlap\
+      \ 90% of A and A _also_ overlaps 90% of B.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--either_overlap"
+    alternatives:
+    - "-e"
+    description: "Require that the minimum fraction be satisfied for A OR B.\n- In\
+      \ other words, if -e is used with -f 0.90 and -F 0.10 this requires\nthat either\
+      \ 90% of A is covered OR 10% of B is covered.\nWithout -e, both fractions would\
+      \ have to be satisfied.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--split"
+    description: "Treat \"split\" BAM or BED12 entries as distinct BED intervals."
+    info: null
+    direction: "input"
+  - type: "file"
+    name: "--genome"
+    alternatives:
+    - "-g"
+    description: "Provide a genome file to enforce consistent chromosome \nsort order\
+      \ across input files. Only applies when used \nwith -sorted option.\n"
+    info: null
+    example:
+    - "genome.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--nonamecheck"
+    description: "For sorted data, don't throw an error if the file \nhas different\
+      \ naming conventions for the same chromosome \n(e.g., \"chr1\" vs \"chr01\"\
+      ).\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--sorted"
+    description: "Use the \"chromsweep\" algorithm for sorted (-k1,1 -k2,2n) input.\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--names"
+    description: "When using multiple databases, provide an alias \nfor each that\
+      \ will appear instead of a fileId when \nalso printing the DB record.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--filenames"
+    description: "When using multiple databases, show each complete filename instead\
+      \ of a fileId when also printing the DB record."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--sortout"
+    description: "When using multiple databases, sort the output DB hits for each\
+      \ record."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--bed"
+    description: "If using BAM input, write output as BED."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--header"
+    description: "Print the header from the A file prior to results."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_buffer_output"
+    alternatives:
+    - "--nobuf"
+    description: "Disable buffered output. Using this option will cause each line\n\
+      of output to be printed as it is generated, rather than saved\nin a buffer.\
+      \ This will make printing large output files \nnoticeably slower, but can be\
+      \ useful in conjunction with\nother software tools and scripts that need to\
+      \ process one\nline of bedtools output at a time.\n"
+    info: null
+    direction: "input"
+  - type: "integer"
+    name: "--io_buffer_size"
+    alternatives:
+    - "--iobuf"
+    description: "Specify amount of memory to use for input buffer.\nTakes an integer\
+      \ argument. Optional suffixes K/M/G supported.\nNote: currently has no effect\
+      \ with compressed files.       \n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "bedtools intersect allows one to screen for overlaps between two sets\
+  \ of genomic features. \nMoreover, it allows one to have fine control as to how\
+  \ the intersections are reported. \nbedtools intersect works with both BED/GFF/VCF\
+  \ and BAM files as input.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+info: null
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "feature intersection"
+- "BAM"
+- "BED"
+- "GFF"
+- "VCF"
+license: "GPL-2.0, MIT"
+references:
+  doi:
+  - "10.1093/bioinformatics/btq033"
+links:
+  repository: "https://github.com/arq5x/bedtools2"
+  documentation: "https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html"
+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_intersect/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/bedtools/bedtools_intersect"
+  executable: "target/executable/bedtools/bedtools_intersect/bedtools_intersect"
+  viash_version: "0.9.0-RC6"
+  git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
+  git_remote: "https://github.com/viash-hub/biobox"
+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-RC6"
+  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_intersect/bedtools_intersect
+++ b/target/executable/bedtools/bedtools_intersect/bedtools_intersect
--- a/target/executable/busco/busco_download_datasets/.config.vsh.yaml
+++ b/target/executable/busco/busco_download_datasets/.config.vsh.yaml
@@ -158,7 +158,7 @@ build_info:
  output: "target/executable/busco/busco_download_datasets"
  executable: "target/executable/busco/busco_download_datasets/busco_download_datasets"
  viash_version: "0.9.0-RC6"
-  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
+  git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/busco/busco_download_datasets/busco_download_datasets
+++ b/target/executable/busco/busco_download_datasets/busco_download_datasets
@@ -474,9 +474,9 @@ 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="2024-07-29T07:58:00Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:22:57Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
+LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
 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
@@ -145,7 +145,7 @@ build_info:
  output: "target/executable/busco/busco_list_datasets"
  executable: "target/executable/busco/busco_list_datasets/busco_list_datasets"
  viash_version: "0.9.0-RC6"
-  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
+  git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/busco/busco_list_datasets/busco_list_datasets
+++ b/target/executable/busco/busco_list_datasets/busco_list_datasets
@@ -464,9 +464,9 @@ 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="2024-07-29T07:58:00Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:22:57Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
+LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
 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
@@ -423,7 +423,7 @@ build_info:
  output: "target/executable/busco/busco_run"
  executable: "target/executable/busco/busco_run/busco_run"
  viash_version: "0.9.0-RC6"
-  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
+  git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/busco/busco_run/busco_run
+++ b/target/executable/busco/busco_run/busco_run
@@ -631,9 +631,9 @@ 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="2024-07-29T07:58:01Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:22:57Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
+LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/cutadapt/.config.vsh.yaml
+++ b/target/executable/cutadapt/.config.vsh.yaml
@@ -740,7 +740,7 @@ build_info:
  output: "target/executable/cutadapt"
  executable: "target/executable/cutadapt/cutadapt"
  viash_version: "0.9.0-RC6"
-  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
+  git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/cutadapt/cutadapt
+++ b/target/executable/cutadapt/cutadapt
@@ -830,9 +830,9 @@ 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="2024-07-29T07:57:59Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:22:55Z"
 LABEL org.opencontainers.image.source="https://github.com/marcelm/cutadapt"
-LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
+LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/falco/.config.vsh.yaml
+++ b/target/executable/falco/.config.vsh.yaml
@@ -317,7 +317,7 @@ build_info:
  output: "target/executable/falco"
  executable: "target/executable/falco/falco"
  viash_version: "0.9.0-RC6"
-  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
+  git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/falco/falco
+++ b/target/executable/falco/falco
@@ -588,9 +588,9 @@ 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="2024-07-29T07:57:59Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:22:56Z"
 LABEL org.opencontainers.image.source="https://github.com/smithlabcode/falco"
-LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
+LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/fastp/.config.vsh.yaml
+++ b/target/executable/fastp/.config.vsh.yaml
@@ -1083,7 +1083,7 @@ build_info:
  output: "target/executable/fastp"
  executable: "target/executable/fastp/fastp"
  viash_version: "0.9.0-RC6"
-  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
+  git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/fastp/fastp
+++ b/target/executable/fastp/fastp
@@ -1027,9 +1027,9 @@ 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="2024-07-29T07:58:04Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:23:01Z"
 LABEL org.opencontainers.image.source="https://github.com/OpenGene/fastp"
-LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
+LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/featurecounts/.config.vsh.yaml
+++ b/target/executable/featurecounts/.config.vsh.yaml
@@ -645,7 +645,7 @@ build_info:
  output: "target/executable/featurecounts"
  executable: "target/executable/featurecounts/featurecounts"
  viash_version: "0.9.0-RC6"
-  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
+  git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/featurecounts/featurecounts
+++ b/target/executable/featurecounts/featurecounts
@@ -753,9 +753,9 @@ 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="2024-07-29T07:58:01Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:22:58Z"
 LABEL org.opencontainers.image.source="https://github.com/ShiLab-Bioinformatics/subread"
-LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
+LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/gffread/.config.vsh.yaml
+++ b/target/executable/gffread/.config.vsh.yaml
@@ -685,7 +685,7 @@ build_info:
  output: "target/executable/gffread"
  executable: "target/executable/gffread/gffread"
  viash_version: "0.9.0-RC6"
-  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
+  git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/gffread/gffread
+++ b/target/executable/gffread/gffread
@@ -806,9 +806,9 @@ 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="2024-07-29T07:58:00Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:22:56Z"
 LABEL org.opencontainers.image.source="https://github.com/gpertea/gffread"
-LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
+LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
 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
@@ -507,7 +507,7 @@ build_info:
  output: "target/executable/lofreq/lofreq_call"
  executable: "target/executable/lofreq/lofreq_call/lofreq_call"
  viash_version: "0.9.0-RC6"
-  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
+  git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/lofreq/lofreq_call/lofreq_call
+++ b/target/executable/lofreq/lofreq_call/lofreq_call
@@ -655,9 +655,9 @@ 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="2024-07-29T07:58:07Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:23:05Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
+LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
 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
@@ -215,7 +215,7 @@ build_info:
  output: "target/executable/lofreq/lofreq_indelqual"
  executable: "target/executable/lofreq/lofreq_indelqual/lofreq_indelqual"
  viash_version: "0.9.0-RC6"
-  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
+  git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual
+++ b/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual
@@ -500,9 +500,9 @@ 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="2024-07-29T07:58:07Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:23:05Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
+LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/multiqc/.config.vsh.yaml
+++ b/target/executable/multiqc/.config.vsh.yaml
@@ -456,7 +456,7 @@ build_info:
  output: "target/executable/multiqc"
  executable: "target/executable/multiqc/multiqc"
  viash_version: "0.9.0-RC6"
-  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
+  git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/multiqc/multiqc
+++ b/target/executable/multiqc/multiqc
@@ -636,9 +636,9 @@ 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="2024-07-29T07:58:02Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:22:59Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
+LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/pear/.config.vsh.yaml
+++ b/target/executable/pear/.config.vsh.yaml
@@ -398,7 +398,7 @@ build_info:
  output: "target/executable/pear"
  executable: "target/executable/pear/pear"
  viash_version: "0.9.0-RC6"
-  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
+  git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/pear/pear
+++ b/target/executable/pear/pear
@@ -596,9 +596,9 @@ 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="2024-07-29T07:58:06Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:23:04Z"
 LABEL org.opencontainers.image.source="https://github.com/tseemann/PEAR"
-LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
+LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/salmon/salmon_index/.config.vsh.yaml
+++ b/target/executable/salmon/salmon_index/.config.vsh.yaml
@@ -277,7 +277,7 @@ build_info:
  output: "target/executable/salmon/salmon_index"
  executable: "target/executable/salmon/salmon_index/salmon_index"
  viash_version: "0.9.0-RC6"
-  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
+  git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/salmon/salmon_index/salmon_index
+++ b/target/executable/salmon/salmon_index/salmon_index
@@ -545,9 +545,9 @@ RUN salmon index -v 2>&1 | sed 's/salmon \([0-9.]*\)/salmon: \1/' > /var/softwar

 LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
 LABEL org.opencontainers.image.description="Companion container for running component salmon salmon_index"
-LABEL org.opencontainers.image.created="2024-07-29T07:58:03Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:23:00Z"
 LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
-LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
+LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/salmon/salmon_quant/.config.vsh.yaml
+++ b/target/executable/salmon/salmon_quant/.config.vsh.yaml
@@ -1173,7 +1173,7 @@ build_info:
  output: "target/executable/salmon/salmon_quant"
  executable: "target/executable/salmon/salmon_quant/salmon_quant"
  viash_version: "0.9.0-RC6"
-  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
+  git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/salmon/salmon_quant/salmon_quant
+++ b/target/executable/salmon/salmon_quant/salmon_quant
@@ -1167,9 +1167,9 @@ RUN salmon index -v 2>&1 | sed 's/salmon \([0-9.]*\)/salmon: \1/' > /var/softwar

 LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
 LABEL org.opencontainers.image.description="Companion container for running component salmon salmon_quant"
-LABEL org.opencontainers.image.created="2024-07-29T07:58:03Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:23:00Z"
 LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
-LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
+LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_collate/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_collate/.config.vsh.yaml
@@ -264,7 +264,7 @@ build_info:
  output: "target/executable/samtools/samtools_collate"
  executable: "target/executable/samtools/samtools_collate/samtools_collate"
  viash_version: "0.9.0-RC6"
-  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
+  git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_collate/samtools_collate
+++ b/target/executable/samtools/samtools_collate/samtools_collate
@@ -518,9 +518,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_collate"
-LABEL org.opencontainers.image.created="2024-07-29T07:58:10Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:23:08Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
+LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_faidx/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_faidx/.config.vsh.yaml
@@ -243,7 +243,7 @@ build_info:
  output: "target/executable/samtools/samtools_faidx"
  executable: "target/executable/samtools/samtools_faidx/samtools_faidx"
  viash_version: "0.9.0-RC6"
-  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
+  git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_faidx/samtools_faidx
+++ b/target/executable/samtools/samtools_faidx/samtools_faidx
@@ -511,9 +511,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_faidx"
-LABEL org.opencontainers.image.created="2024-07-29T07:58:11Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:23:09Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
+LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_fasta/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_fasta/.config.vsh.yaml
@@ -433,7 +433,7 @@ build_info:
  output: "target/executable/samtools/samtools_fasta"
  executable: "target/executable/samtools/samtools_fasta/samtools_fasta"
  viash_version: "0.9.0-RC6"
-  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
+  git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_fasta/samtools_fasta
+++ b/target/executable/samtools/samtools_fasta/samtools_fasta
@@ -624,9 +624,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_fasta"
-LABEL org.opencontainers.image.created="2024-07-29T07:58:08Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:23:07Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
+LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_fastq/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_fastq/.config.vsh.yaml
@@ -433,7 +433,7 @@ build_info:
  output: "target/executable/samtools/samtools_fastq"
  executable: "target/executable/samtools/samtools_fastq/samtools_fastq"
  viash_version: "0.9.0-RC6"
-  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
+  git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_fastq/samtools_fastq
+++ b/target/executable/samtools/samtools_fastq/samtools_fastq
@@ -625,9 +625,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_fastq"
-LABEL org.opencontainers.image.created="2024-07-29T07:58:11Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:23:09Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
+LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_flagstat/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_flagstat/.config.vsh.yaml
@@ -173,7 +173,7 @@ build_info:
  output: "target/executable/samtools/samtools_flagstat"
  executable: "target/executable/samtools/samtools_flagstat/samtools_flagstat"
  viash_version: "0.9.0-RC6"
-  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
+  git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_flagstat/samtools_flagstat
+++ b/target/executable/samtools/samtools_flagstat/samtools_flagstat
@@ -473,9 +473,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_flagstat"
-LABEL org.opencontainers.image.created="2024-07-29T07:58:09Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:23:07Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
+LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_idxstats/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_idxstats/.config.vsh.yaml
@@ -183,7 +183,7 @@ build_info:
  output: "target/executable/samtools/samtools_idxstats"
  executable: "target/executable/samtools/samtools_idxstats/samtools_idxstats"
  viash_version: "0.9.0-RC6"
-  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
+  git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_idxstats/samtools_idxstats
+++ b/target/executable/samtools/samtools_idxstats/samtools_idxstats
@@ -477,9 +477,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_idxstats"
-LABEL org.opencontainers.image.created="2024-07-29T07:58:09Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:23:08Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
+LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_index/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_index/.config.vsh.yaml
@@ -189,7 +189,7 @@ build_info:
  output: "target/executable/samtools/samtools_index"
  executable: "target/executable/samtools/samtools_index/samtools_index"
  viash_version: "0.9.0-RC6"
-  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
+  git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_index/samtools_index
+++ b/target/executable/samtools/samtools_index/samtools_index
@@ -484,9 +484,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_index"
-LABEL org.opencontainers.image.created="2024-07-29T07:58:10Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:23:08Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
+LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_sort/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_sort/.config.vsh.yaml
@@ -332,7 +332,7 @@ build_info:
  output: "target/executable/samtools/samtools_sort"
  executable: "target/executable/samtools/samtools_sort/samtools_sort"
  viash_version: "0.9.0-RC6"
-  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
+  git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_sort/samtools_sort
+++ b/target/executable/samtools/samtools_sort/samtools_sort
@@ -555,9 +555,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_sort"
-LABEL org.opencontainers.image.created="2024-07-29T07:58:10Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:23:09Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
+LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_stats/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_stats/.config.vsh.yaml
@@ -401,7 +401,7 @@ build_info:
  output: "target/executable/samtools/samtools_stats"
  executable: "target/executable/samtools/samtools_stats/samtools_stats"
  viash_version: "0.9.0-RC6"
-  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
+  git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_stats/samtools_stats
+++ b/target/executable/samtools/samtools_stats/samtools_stats
@@ -574,9 +574,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_stats"
-LABEL org.opencontainers.image.created="2024-07-29T07:58:09Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:23:07Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
+LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/samtools/samtools_view/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_view/.config.vsh.yaml
@@ -665,7 +665,7 @@ build_info:
  output: "target/executable/samtools/samtools_view"
  executable: "target/executable/samtools/samtools_view/samtools_view"
  viash_version: "0.9.0-RC6"
-  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
+  git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/samtools/samtools_view/samtools_view
+++ b/target/executable/samtools/samtools_view/samtools_view
@@ -824,9 +824,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_view"
-LABEL org.opencontainers.image.created="2024-07-29T07:58:08Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:23:06Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
+LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/seqtk/seqtk_sample/.config.vsh.yaml
+++ b/target/executable/seqtk/seqtk_sample/.config.vsh.yaml
@@ -173,7 +173,7 @@ build_info:
  output: "target/executable/seqtk/seqtk_sample"
  executable: "target/executable/seqtk/seqtk_sample/seqtk_sample"
  viash_version: "0.9.0-RC6"
-  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
+  git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/seqtk/seqtk_sample/seqtk_sample
+++ b/target/executable/seqtk/seqtk_sample/seqtk_sample
@@ -480,9 +480,9 @@ FROM quay.io/biocontainers/seqtk:1.4--he4a0461_2
 ENTRYPOINT []
 LABEL org.opencontainers.image.authors="Jakub Majercik"
 LABEL org.opencontainers.image.description="Companion container for running component seqtk seqtk_sample"
-LABEL org.opencontainers.image.created="2024-07-29T07:58:05Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:23:02Z"
 LABEL org.opencontainers.image.source="https://github.com/lh3/seqtk/tree/v1.4"
-LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
+LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml
+++ b/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml
@@ -196,7 +196,7 @@ build_info:
  output: "target/executable/seqtk/seqtk_subseq"
  executable: "target/executable/seqtk/seqtk_subseq/seqtk_subseq"
  viash_version: "0.9.0-RC6"
-  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
+  git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/seqtk/seqtk_subseq/seqtk_subseq
+++ b/target/executable/seqtk/seqtk_subseq/seqtk_subseq
@@ -490,9 +490,9 @@ RUN echo $(echo $(seqtk 2>&1) | sed -n 's/.*\(Version: [^ ]*\).*/\1/p') > /var/s

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component seqtk seqtk_subseq"
-LABEL org.opencontainers.image.created="2024-07-29T07:58:05Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:23:02Z"
 LABEL org.opencontainers.image.source="https://github.com/lh3/seqtk/tree/v1.4"
-LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
+LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/star/star_align_reads/.config.vsh.yaml
+++ b/target/executable/star/star_align_reads/.config.vsh.yaml
@@ -2663,7 +2663,7 @@ build_info:
  output: "target/executable/star/star_align_reads"
  executable: "target/executable/star/star_align_reads/star_align_reads"
  viash_version: "0.9.0-RC6"
-  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
+  git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/star/star_align_reads/star_align_reads
+++ b/target/executable/star/star_align_reads/star_align_reads
@@ -1919,9 +1919,9 @@ RUN STAR --version | sed 's#\(.*\)#star: "\1"#' > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component star star_align_reads"
-LABEL org.opencontainers.image.created="2024-07-29T07:58:05Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:23:03Z"
 LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR"
-LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
+LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/star/star_genome_generate/.config.vsh.yaml
+++ b/target/executable/star/star_genome_generate/.config.vsh.yaml
@@ -333,7 +333,7 @@ build_info:
  output: "target/executable/star/star_genome_generate"
  executable: "target/executable/star/star_genome_generate/star_genome_generate"
  viash_version: "0.9.0-RC6"
-  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
+  git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/star/star_genome_generate/star_genome_generate
+++ b/target/executable/star/star_genome_generate/star_genome_generate
@@ -576,9 +576,9 @@ RUN STAR --version | sed 's#\(.*\)#star: "\1"#' > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
 LABEL org.opencontainers.image.description="Companion container for running component star star_genome_generate"
-LABEL org.opencontainers.image.created="2024-07-29T07:58:05Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:23:03Z"
 LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR"
-LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
+LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml
+++ b/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml
@@ -611,7 +611,7 @@ build_info:
  output: "target/executable/umi_tools/umi_tools_dedup"
  executable: "target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup"
  viash_version: "0.9.0-RC6"
-  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
+  git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup
+++ b/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup
@@ -769,9 +769,9 @@ RUN umi_tools -v | sed 's/ version//g' > /var/software_versions.txt

 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component umi_tools umi_tools_dedup"
-LABEL org.opencontainers.image.created="2024-07-29T07:58:11Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:23:10Z"
 LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools"
-LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
+LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml
+++ b/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml
@@ -449,7 +449,7 @@ build_info:
  output: "target/executable/umi_tools/umi_tools_extract"
  executable: "target/executable/umi_tools/umi_tools_extract/umi_tools_extract"
  viash_version: "0.9.0-RC6"
-  git_commit: "da414e72c60758895b16818309d6c147c288dd84"
+  git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/umi_tools/umi_tools_extract/umi_tools_extract
+++ b/target/executable/umi_tools/umi_tools_extract/umi_tools_extract
@@ -636,9 +636,9 @@ ENTRYPOINT []
 RUN umi_tools -v | sed 's/ version//g' > /var/software_versions.txt

 LABEL org.opencontainers.image.description="Companion container for running component umi_tools umi_tools_extract"
-LABEL org.opencontainers.image.created="2024-07-29T07:58:12Z"
+LABEL org.opencontainers.image.created="2024-07-31T19:23:10Z"
 LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools"
-LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
+LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER