Build branch bump_viash_0_9_4 with version bump_viash_0_9_4 (be1cd83)

Build pipeline: viash-hub.biobox.bump-viash-0-9-4-275jj

Source commit: be1cd83dd6

Source message: Add PR number

target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml

@@ -0,0 +1,265 @@
+name: "agat_convert_bed2gff"
+namespace: "agat"
+version: "bump_viash_0_9_4"
+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: "--bed"
+    description: "Input bed file that will be converted."
+    info: null
+    example:
+    - "input.bed"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    alternatives:
+    - "-o"
+    - "--out"
+    - "--outfile"
+    - "--gff"
+    description: "Output GFF file. If no output file is specified, the output will\
+      \ be written to STDOUT."
+    info: null
+    example:
+    - "output.gff"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Arguments"
+  arguments:
+  - type: "string"
+    name: "--source"
+    description: "The source informs about the tool used to produce the data and is\
+      \ stored in 2nd field of a gff file. Example: Stringtie, Maker, Augustus, etc.\
+      \ [default: data]\n"
+    info: null
+    example:
+    - "Stringtie"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--primary_tag"
+    description: "The primary_tag corresponds to the data type and is stored in 3rd\
+      \ field of a gff file. Example: gene, mRNA, CDS, etc. [default: gene]\n"
+    info: null
+    example:
+    - "gene"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--inflate_off"
+    description: "By default we inflate the block fields (blockCount, blockSizes,\
+      \ blockStarts) to create subfeatures of the main feature (primary_tag). The\
+      \ type of subfeature created is based on the inflate_type parameter. If you\
+      \ do not want this inflating behaviour you can deactivate it by using the --inflate_off\
+      \ option.\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--inflate_type"
+    description: "Feature type (3rd column in gff) created when inflate parameter\
+      \ activated [default: exon].\n"
+    info: null
+    example:
+    - "exon"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--verbose"
+    description: "add verbosity"
+    info: null
+    direction: "input"
+  - type: "file"
+    name: "--config"
+    alternatives:
+    - "-c"
+    description: "Input agat config file. By default AGAT takes as input agat_config.yaml\
+      \ file from the working directory if any, otherwise it takes the orignal agat_config.yaml\
+      \ shipped with AGAT. To get the agat_config.yaml locally type: \"agat config\
+      \ --expose\". The --config option gives you the possibility to use your own\
+      \ AGAT config file (located elsewhere 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: "The script takes a bed file as input, and will translate it in gff format.\
+  \ The BED format is described here The script converts 0-based, half-open [start-1,\
+  \ end) bed file to 1-based, closed [start, end] General Feature Format v3 (GFF3).\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test_data"
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "gene annotations"
+- "GFF conversion"
+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_convert_bed2gff.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: "bump_viash_0_9_4"
+  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_convert_bed2gff/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/agat/agat_convert_bed2gff"
+  executable: "target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml

@@ -0,0 +1,255 @@
+name: "agat_convert_embl2gff"
+namespace: "agat"
+version: "bump_viash_0_9_4"
+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: "--embl"
+    description: "Input EMBL file that will be read."
+    info: null
+    example:
+    - "input.embl"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    alternatives:
+    - "-o"
+    - "--out"
+    - "--outfile"
+    - "--gff"
+    description: "Output GFF file. If no output file is specified, the output will\
+      \ be written to STDOUT."
+    info: null
+    example:
+    - "output.gff"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Arguments"
+  arguments:
+  - type: "boolean_true"
+    name: "--emblmygff3"
+    description: "Means that the EMBL flat file comes from the EMBLmyGFF3 software.\
+      \ This is an EMBL format dedicated for submission and contains particularity\
+      \ to deal with. This parameter is needed to get a proper sequence id in the\
+      \ GFF3 from an embl made with EMBLmyGFF3.\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--primary_tag"
+    alternatives:
+    - "--pt"
+    - "-t"
+    description: "List of \"primary tag\". Useful to discard or keep specific features.\
+      \ Multiple tags must be comma-separated.\n"
+    info: null
+    example:
+    - "tag1"
+    - "tag2"
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--discard"
+    alternatives:
+    - "-d"
+    description: "Means that primary tags provided by the option \"primary_tag\" will\
+      \ be discarded.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--keep"
+    alternatives:
+    - "-k"
+    description: "Means that only primary tags provided by the option \"primary_tag\"\
+      \ will be kept.\n"
+    info: null
+    direction: "input"
+  - type: "file"
+    name: "--config"
+    alternatives:
+    - "-c"
+    description: "Input agat config file. By default AGAT takes as input agat_config.yaml\
+      \ file from the working directory if any, otherwise it takes the original agat_config.yaml\
+      \ shipped with AGAT. To get the agat_config.yaml locally type: \"agat config\
+      \ --expose\". The --config option gives you the possibility to use your own\
+      \ AGAT config file (located elsewhere 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: "The script takes an EMBL file as input, and will translate it in gff\
+  \ format.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test_data"
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "gene annotations"
+- "GFF conversion"
+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_convert_embl2gff.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: "bump_viash_0_9_4"
+  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_convert_embl2gff/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/agat/agat_convert_embl2gff"
+  executable: "target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/agat/agat_convert_genscan2gff/.config.vsh.yaml

@@ -0,0 +1,260 @@
+name: "agat_convert_genscan2gff"
+namespace: "agat"
+version: "bump_viash_0_9_4"
+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: "--genscan"
+    alternatives:
+    - "-g"
+    description: "Input genscan bed file that will be converted."
+    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"
+    - "--out"
+    - "--outfile"
+    - "--gff"
+    description: "Output GFF file. If no output file is specified, the output will\
+      \ be written to STDOUT."
+    info: null
+    example:
+    - "output.gff"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Arguments"
+  arguments:
+  - type: "string"
+    name: "--source"
+    description: "The source informs about the tool used to produce the data and is\
+      \ stored in 2nd field of a gff file. Example: Stringtie, Maker, Augustus, etc.\
+      \ [default: data]\n"
+    info: null
+    example:
+    - "Stringtie"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--primary_tag"
+    description: "The primary_tag corresponds to the data type and is stored in 3rd\
+      \ field of a gff file. Example: gene, mRNA, CDS, etc. [default: gene]\n"
+    info: null
+    example:
+    - "gene"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--inflate_type"
+    description: "Feature type (3rd column in gff) created when inflate parameter\
+      \ activated [default: exon].\n"
+    info: null
+    example:
+    - "exon"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--verbose"
+    description: "add verbosity"
+    info: null
+    direction: "input"
+  - type: "file"
+    name: "--config"
+    alternatives:
+    - "-c"
+    description: "AGAT config file. By default AGAT takes the original agat_config.yaml\
+      \ shipped with AGAT. The `--config` option gives you the possibility to use\
+      \ your own AGAT config file (located elsewhere 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: "The script takes a GENSCAN file as input, and will translate it in gff\n\
+  format. The GENSCAN format is described [here](http://genome.crg.es/courses/Bioinformatics2003_genefinding/results/genscan.html).\n\
+  \n**Known problem** \n\nYou must have submited only DNA sequence, without any header!!\
+  \ Indeed the tool expects only DNA\nsequences and does not crash/warn if an header\
+  \ is submited along the\nsequence. e.g If you have an header \">seq\" s-e-q are\
+  \ seen as the 3 first\nnucleotides of the sequence. Then all prediction location\
+  \ are shifted\naccordingly. (checked only on the [online version](http://argonaute.mit.edu/GENSCAN.html).\
+  \ \nI don't know if there is the same problem elsewhere.)\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test_data"
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "gene annotations"
+- "GFF conversion"
+- "GENSCAN"
+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_convert_genscan2gff.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: "bump_viash_0_9_4"
+  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_convert_genscan2gff/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/agat/agat_convert_genscan2gff"
+  executable: "target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/agat/agat_convert_mfannot2gff/.config.vsh.yaml

@@ -0,0 +1,216 @@
+name: "agat_convert_mfannot2gff"
+namespace: "agat"
+version: "bump_viash_0_9_4"
+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: "--mfannot"
+    alternatives:
+    - "-m"
+    - "-i"
+    description: "The mfannot input file."
+    info: null
+    example:
+    - "input.mfannot"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--gff"
+    alternatives:
+    - "-g"
+    - "-o"
+    description: "The GFF output file."
+    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. The `--config` option gives you the possibility to use\
+      \ your own AGAT config file (located elsewhere 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: "Conversion utility for MFannot \"masterfile\" annotation produced by\
+  \ the\n[MFannot pipeline](http://megasun.bch.umontreal.ca/RNAweasel/). Reports\n\
+  GFF3 format.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test_data"
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "gene annotations"
+- "GFF"
+- "Mfannot"
+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_convert_mfannot2gff.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: "bump_viash_0_9_4"
+  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_convert_mfannot2gff/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/agat/agat_convert_mfannot2gff"
+  executable: "target/executable/agat/agat_convert_mfannot2gff/agat_convert_mfannot2gff"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml

@@ -0,0 +1,258 @@
+name: "agat_convert_sp_gff2gtf"
+namespace: "agat"
+version: "bump_viash_0_9_4"
+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:
+    - "-i"
+    description: "Input GFF/GTF file that will be read"
+    info: null
+    example:
+    - "input.gff"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    alternatives:
+    - "-o"
+    - "--out"
+    - "--outfile"
+    - "--gtf"
+    description: "Output GTF file. If no output file is specified, the output will\
+      \ be written to STDOUT."
+    info: null
+    example:
+    - "output.gtf"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Arguments"
+  arguments:
+  - type: "string"
+    name: "--gtf_version"
+    description: "Version of the GTF output (1,2,2.1,2.2,2.5,3 or relax). Default\
+      \ value from AGAT config file (relax for the default config). The script option\
+      \ has the higher priority.  \n\n  * relax: all feature types are accepted. \
+      \ \n  * GTF3 (9 feature types accepted): gene, transcript, exon, CDS, Selenocysteine,\
+      \ start_codon, stop_codon, three_prime_utr and five_prime_utr.  \n  * GTF2.5\
+      \ (8 feature types accepted): gene, transcript, exon, CDS, UTR, start_codon,\
+      \ stop_codon, Selenocysteine.  \n  * GTF2.2 (9 feature types accepted): CDS,\
+      \ start_codon, stop_codon, 5UTR, 3UTR, inter, inter_CNS, intron_CNS and exon.\
+      \  \n  * GTF2.1 (6 feature types accepted): CDS, start_codon, stop_codon, exon,\
+      \ 5UTR, 3UTR.  \n  * GTF2 (4 feature types accepted): CDS, start_codon, stop_codon,\
+      \ exon.  \n  * GTF1 (5 feature types accepted): CDS, start_codon, stop_codon,\
+      \ exon, intron.  \n"
+    info: null
+    example:
+    - "3"
+    required: false
+    choices:
+    - "relax"
+    - "1"
+    - "2"
+    - "2.1"
+    - "2.2"
+    - "2.5"
+    - "3"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--config"
+    alternatives:
+    - "-c"
+    description: "Input agat config file. By default AGAT takes as input agat_config.yaml\
+      \ file from the working directory if any, otherwise it takes the orignal agat_config.yaml\
+      \ shipped with AGAT. To get the agat_config.yaml locally type: \"agat config\
+      \ --expose\". The --config option gives you the possibility to use your own\
+      \ AGAT config file (located elsewhere 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: "The script aims to convert any GTF/GFF file into a proper GTF file.\
+  \ Full\ninformation about the format can be found here:\nhttps://agat.readthedocs.io/en/latest/gxf.html\
+  \ You can choose among 7\ndifferent GTF types (1, 2, 2.1, 2.2, 2.5, 3 or relax).\
+  \ Depending the\nversion selected the script will filter out the features that are\
+  \ not\naccepted. For GTF2.5 and 3, every level1 feature (e.g nc_gene\npseudogene)\
+  \ will be converted into gene feature and every level2 feature\n(e.g mRNA ncRNA)\
+  \ will be converted into transcript feature. Using the\n\"relax\" option you will\
+  \ produce a GTF-like output keeping all original\nfeature types (3rd column). No\
+  \ modification will occur e.g. mRNA to\ntranscript.\n\nTo be fully GTF compliant\
+  \ all feature have a gene_id and a transcript_id\nattribute. The gene_id is unique\
+  \ identifier for the genomic source of\nthe transcript, which is used to group transcripts\
+  \ into genes. The\ntranscript_id is a unique identifier for the predicted transcript,\
+  \ which\nis used to group features into transcripts.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test_data"
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "gene annotations"
+- "GTF conversion"
+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/"
+  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: "bump_viash_0_9_4"
+  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_convert_sp_gff2gtf/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/agat/agat_convert_sp_gff2gtf"
+  executable: "target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml

@@ -0,0 +1,218 @@
+name: "agat_convert_sp_gff2tsv"
+namespace: "agat"
+version: "bump_viash_0_9_4"
+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."
+    info: null
+    example:
+    - "input.gff"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    alternatives:
+    - "-o"
+    - "--out"
+    - "--outfile"
+    description: "Output GFF file. If no output file is specified, the output will\
+      \ be written to STDOUT."
+    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: "String - Input agat config file. By default AGAT takes as input\n\
+      agat_config.yaml file from the working directory if any,\notherwise it takes\
+      \ the orignal agat_config.yaml shipped with\nAGAT. To get the agat_config.yaml\
+      \ locally type: \"agat config\n--expose\". The --config option gives you the\
+      \ possibility to use\nyour own AGAT config file (located elsewhere or named\n\
+      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: "The script aims to convert gtf/gff file into tabulated file. Attribute's\n\
+  tags from the 9th column become column titles.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test_data"
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "gene annotations"
+- "GFF conversion"
+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_convert_sp_gff2tsv.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: "bump_viash_0_9_4"
+  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_convert_sp_gff2tsv/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/agat/agat_convert_sp_gff2tsv"
+  executable: "target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml

@@ -0,0 +1,225 @@
+name: "agat_convert_sp_gxf2gxf"
+namespace: "agat"
+version: "bump_viash_0_9_4"
+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: "--gxf"
+    alternatives:
+    - "-g"
+    - "--gtf"
+    - "--gff"
+    description: "String - Input GTF/GFF file. Compressed file with .gz extension\
+      \ is accepted.\n"
+    info: null
+    example:
+    - "input.gff"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    alternatives:
+    - "-o"
+    description: "String - Output GFF file. If no output file is specified, the output\
+      \ will be written to STDOUT.\n"
+    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: "String - Input agat config file. By default AGAT takes as input\
+      \ agat_config.yaml file from the working directory if any, otherwise it takes\
+      \ the original agat_config.yaml shipped with AGAT. To get the agat_config.yaml\
+      \ locally type: \"agat config --expose\". The --config option gives you the\
+      \ possibility to use your own AGAT config file (located elsewhere 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: "This script fixes and/or standardizes any GTF/GFF file into full sorted\n\
+  GTF/GFF file. It AGAT parser removes duplicate features, fixes\nduplicated IDs,\
+  \ adds missing ID and/or Parent attributes, deflates\nfactorized attributes (attributes\
+  \ with several parents are duplicated\nwith uniq ID), add missing features when\
+  \ possible (e.g. add exon if only\nCDS described, add UTR if CDS and exon described),\
+  \ fix feature locations\n(e.g. check exon is embedded in the parent features mRNA,\
+  \ gene), etc...\n\nAll AGAT's scripts with the _sp_ prefix use the AGAT parser,\
+  \ before to\nperform any supplementary task. So, it is not necessary to run this\n\
+  script prior the use of any other _sp_ script.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test_data"
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "gene annotations"
+- "GFF conversion"
+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_convert_sp_gxf2gxf.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: "bump_viash_0_9_4"
+  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_convert_sp_gxf2gxf/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/agat/agat_convert_sp_gxf2gxf"
+  executable: "target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/agat/agat_sp_add_introns/.config.vsh.yaml

@@ -0,0 +1,216 @@
+name: "agat_sp_add_introns"
+namespace: "agat"
+version: "bump_viash_0_9_4"
+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 GTF/GFF file."
+    info: null
+    example:
+    - "input.gff"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    alternatives:
+    - "-o"
+    - "--out"
+    - "--outfile"
+    - "--gtf"
+    description: "Output GFF3 file."
+    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. The `--config` option \ngives you the possibility to use\
+      \ your own AGAT config file (located elsewhere 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: "Add intronic elements to a gtf/gff file without intron features.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test_data"
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "gene annotations"
+- "GTF conversion"
+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_add_introns.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: "bump_viash_0_9_4"
+  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_add_introns/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/agat/agat_sp_add_introns"
+  executable: "target/executable/agat/agat_sp_add_introns/agat_sp_add_introns"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/agat/agat_sp_filter_feature_from_kill_list/.config.vsh.yaml

@@ -0,0 +1,266 @@
+name: "agat_sp_filter_feature_from_kill_list"
+namespace: "agat"
+version: "bump_viash_0_9_4"
+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"
+scope:
+  image: "public"
+  target: "public"
+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: "bump_viash_0_9_4"
+  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: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/agat/agat_sp_merge_annotations/.config.vsh.yaml

@@ -0,0 +1,214 @@
+name: "agat_sp_merge_annotations"
+namespace: "agat"
+version: "bump_viash_0_9_4"
+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"
+scope:
+  image: "public"
+  target: "public"
+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: "bump_viash_0_9_4"
+  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: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/agat/agat_sp_statistics/.config.vsh.yaml

@@ -0,0 +1,261 @@
+name: "agat_sp_statistics"
+namespace: "agat"
+version: "bump_viash_0_9_4"
+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:
+    - "-i"
+    description: "Input GTF/GFF file."
+    info: null
+    example:
+    - "input.gff"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--gs_fasta"
+    description: "Genome size directly from a fasta file to compute more statistics.\n"
+    info: null
+    example:
+    - "genome.fasta"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    alternatives:
+    - "-o"
+    description: "The file where the results will be written.\n"
+    info: null
+    example:
+    - "output.txt"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Options"
+  arguments:
+  - type: "boolean_true"
+    name: "--plot"
+    alternatives:
+    - "-p"
+    - "-d"
+    description: "When this option is used, an histogram of distribution of the features\
+      \ will be printed in pdf files.\n"
+    info: null
+    direction: "input"
+  - type: "integer"
+    name: "--gs_size"
+    description: "Genome size in nucleotides to compute more statistics.\n"
+    info: null
+    example:
+    - 1000000
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--verbose"
+    alternatives:
+    - "-v"
+    description: "Verbose option. To modify verbosity. Default is 1. 0 is quiet, 2\
+      \ and 3 are increasing verbosity.\n"
+    info: null
+    example:
+    - 1
+    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. The `--config`\noption gives you the possibility to use\
+      \ your own AGAT config file (located elsewhere 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: "The script provides exhaustive statistics of a gft/gff file. \n\nIf\
+  \ you have isoforms in your file, even if correct, some values calculated\nmight\
+  \ sounds incoherent: e.g. total length mRNA can be superior than the\ngenome size.\
+  \ Because all isoforms length is added... It is why by\ndefault we always compute\
+  \ the statistics twice when there are isoforms,\nonce with the isoforms, once without\
+  \ (In that case we keep the longest\nisoform per locus).\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test_data"
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "gene annotations"
+- "statistics"
+- "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_statistics.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: "bump_viash_0_9_4"
+  namespace_separator: "/"
+  setup:
+  - type: "docker"
+    run:
+    - "agat --version | sed 's/.*v\\.//; s/\\s.*//' | sed 's/^/AGAT: /' > /var/software_versions.txt\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/agat/agat_sp_statistics/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/agat/agat_sp_statistics"
+  executable: "target/executable/agat/agat_sp_statistics/agat_sp_statistics"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/agat/agat_sq_stat_basic/.config.vsh.yaml

@@ -0,0 +1,257 @@
+name: "agat_sq_stat_basic"
+namespace: "agat"
+version: "bump_viash_0_9_4"
+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:
+    - "-i"
+    - "--file"
+    - "--input"
+    description: "Input GTF/GFF file.\n"
+    info: null
+    example:
+    - "input.gff"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--genome_size"
+    alternatives:
+    - "-g"
+    description: "That input is designed to know the genome size in order to calculate\
+      \ the percentage of the genome represented by each kind of feature type. You\
+      \ can provide an INTEGER. Or you can also pass a fasta file using the argument\
+      \ --genome_size_fasta. If both are provided, only the value of --genome_size\
+      \ will be considered.\n"
+    info: null
+    example:
+    - 10000
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--genome_size_fasta"
+    description: "That input is designed to know the genome size in order to calculate\
+      \ the percentage of the genome represented by each kind of feature type. You\
+      \ can provide the genome in fasta format. Or you can also pass the size directly\
+      \ as an integer using the argument --genome_size. If you provide the fasta,\
+      \ the genome size will be calculated on the fly. If both are provided, only\
+      \ the value of --genome_size will be considered.\n"
+    info: null
+    example:
+    - "genome.fasta"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    alternatives:
+    - "-o"
+    description: "Output file. The result is in tabulate format.\n"
+    info: null
+    example:
+    - "output.txt"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Arguments"
+  arguments:
+  - type: "boolean_true"
+    name: "--inflate"
+    description: "Inflate the statistics taking into account feature with\nmulti-parents.\
+      \ Indeed to avoid redundant information, some gff\nfactorize identical features.\
+      \ e.g: one exon used in two\ndifferent isoform will be defined only once, and\
+      \ will have\nmultiple parent. By default the script count such feature only\n\
+      once. Using the inflate option allows to count the feature and\nits size as\
+      \ many time there are parents.\n"
+    info: null
+    direction: "input"
+  - type: "file"
+    name: "--config"
+    alternatives:
+    - "-c"
+    description: "AGAT config file. By default AGAT takes the original agat_config.yaml\
+      \ shipped with AGAT. The `--config` option gives you the possibility to use\
+      \ your own AGAT config file (located elsewhere 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: "The script aims to provide basic statistics of a gtf/gff file.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test_data"
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "gene annotations"
+- "gff"
+- "statistics"
+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_sq_stat_basic.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: "bump_viash_0_9_4"
+  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_sq_stat_basic/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/agat/agat_sq_stat_basic"
+  executable: "target/executable/agat/agat_sq_stat_basic/agat_sq_stat_basic"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/arriba/.config.vsh.yaml

@@ -0,0 +1,736 @@
+name: "arriba"
+version: "bump_viash_0_9_4"
+authors:
+- name: "Robrecht Cannoodt"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "robrecht@data-intuitive.com"
+      github: "rcannood"
+      orcid: "0000-0003-3641-729X"
+      linkedin: "robrechtcannoodt"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Science Engineer"
+    - name: "Open Problems"
+      href: "https://openproblems.bio"
+      role: "Core Member"
+argument_groups:
+- name: "Inputs"
+  arguments:
+  - type: "file"
+    name: "--bam"
+    alternatives:
+    - "-x"
+    description: "File in SAM/BAM/CRAM format with main alignments as generated by\
+      \ STAR\n(Aligned.out.sam). Arriba extracts candidate reads from this file.\n"
+    info: null
+    example:
+    - "Aligned.out.bam"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--genome"
+    alternatives:
+    - "-a"
+    description: "FastA file with genome sequence (assembly). The file may be gzip-compressed.\
+      \ An \nindex with the file extension .fai must exist only if CRAM files are\
+      \ processed.\n"
+    info: null
+    example:
+    - "assembly.fa"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--gene_annotation"
+    alternatives:
+    - "-g"
+    description: "GTF file with gene annotation. The file may be gzip-compressed.\n"
+    info: null
+    example:
+    - "annotation.gtf"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--known_fusions"
+    alternatives:
+    - "-k"
+    description: "File containing known/recurrent fusions. Some cancer entities are\
+      \ often \ncharacterized by fusions between the same pair of genes. In order\
+      \ to boost \nsensitivity, a list of known fusions can be supplied using this\
+      \ parameter. The list \nmust contain two columns with the names of the fused\
+      \ genes, separated by tabs.\n"
+    info: null
+    example:
+    - "known_fusions.tsv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--blacklist"
+    alternatives:
+    - "-b"
+    description: "File containing blacklisted events (recurrent artifacts and transcripts\
+      \ \nobserved in healthy tissue).\n"
+    info: null
+    example:
+    - "blacklist.tsv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--structural_variants"
+    alternatives:
+    - "-d"
+    description: "Tab-separated file with coordinates of structural variants found\
+      \ using \nwhole-genome sequencing data. These coordinates serve to increase\
+      \ sensitivity \ntowards weakly expressed fusions and to eliminate fusions with\
+      \ low evidence. \n"
+    info: null
+    example:
+    - "structural_variants_from_WGS.tsv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--tags"
+    alternatives:
+    - "-t"
+    description: "Tab-separated file containing fusions to annotate with tags in the\
+      \ 'tags' column. \nThe first two columns specify the genes; the third column\
+      \ specifies the tag. The \nfile may be gzip-compressed. \n"
+    info: null
+    example:
+    - "tags.tsv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--protein_domains"
+    alternatives:
+    - "-p"
+    description: "File in GFF3 format containing coordinates of the protein domains\
+      \ of genes. The\nprotein domains retained in a fusion are listed in the column\n\
+      'retained_protein_domains'. The file may be gzip-compressed.\n"
+    info: null
+    example:
+    - "protein_domains.gff3"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--fusions"
+    alternatives:
+    - "-o"
+    description: "Output file with fusions that have passed all filters.\n"
+    info: null
+    example:
+    - "fusions.tsv"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--fusions_discarded"
+    alternatives:
+    - "-O"
+    description: "Output file with fusions that were discarded due to filtering. \n"
+    info: null
+    example:
+    - "fusions.discarded.tsv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Arguments"
+  arguments:
+  - type: "long"
+    name: "--max_genomic_breakpoint_distance"
+    alternatives:
+    - "-D"
+    description: "When a file with genomic breakpoints obtained via \nwhole-genome\
+      \ sequencing is supplied via the --structural_variants\nparameter, this parameter\
+      \ determines how far a \ngenomic breakpoint may be away from a \ntranscriptomic\
+      \ breakpoint to consider it as a \nrelated event. For events inside genes, the\
+      \ \ndistance is added to the end of the gene; for \nintergenic events, the distance\
+      \ threshold is \napplied as is. Default: 100000.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--strandedness"
+    alternatives:
+    - "-s"
+    description: "Whether a strand-specific protocol was used for library preparation,\
+      \ \nand if so, the type of strandedness (auto/yes/no/reverse). When \nunstranded\
+      \ data is processed, the strand can sometimes be inferred from \nsplice-patterns.\
+      \ But in unclear situations, stranded data helps \nresolve ambiguities. Default:\
+      \ auto\n"
+    info: null
+    required: false
+    choices:
+    - "auto"
+    - "yes"
+    - "no"
+    - "reverse"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--interesting_contigs"
+    alternatives:
+    - "-i"
+    description: "List of interesting contigs. Fusions between genes \non other contigs\
+      \ are ignored. Contigs can be specified with or without the \nprefix \"chr\"\
+      . Asterisks (*) are treated as wild-cards. \nDefault: 1 2 3 4 5 6 7 8 9 10 11\
+      \ 12 13 14 15 16 17 18 19 20 21 22 X Y AC_* NC_*\n"
+    info: null
+    example:
+    - "1"
+    - "2"
+    - "AC_*"
+    - "NC_*"
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+  - type: "string"
+    name: "--viral_contigs"
+    alternatives:
+    - "-v"
+    description: "List of viral contigs. Asterisks (*) are treated as \nwild-cards.\n\
+      Default: AC_* NC_*\n"
+    info: null
+    example:
+    - "AC_*"
+    - "NC_*"
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+  - type: "string"
+    name: "--disable_filters"
+    alternatives:
+    - "-f"
+    description: "List of filters to disable. By default all filters are \nenabled.\
+      \ \n"
+    info: null
+    required: false
+    choices:
+    - "homologs"
+    - "low_entropy"
+    - "isoforms"
+    - "top_expressed_viral_contigs"
+    - "viral_contigs"
+    - "uninteresting_contigs"
+    - "non_coding_neighbors"
+    - "mismatches"
+    - "duplicates"
+    - "no_genomic_support"
+    - "genomic_support"
+    - "intronic"
+    - "end_to_end"
+    - "relative_support"
+    - "low_coverage_viral_contigs"
+    - "merge_adjacent"
+    - "mismappers"
+    - "multimappers"
+    - "same_gene"
+    - "long_gap"
+    - "internal_tandem_duplication"
+    - "small_insert_size"
+    - "read_through"
+    - "inconsistently_clipped"
+    - "intragenic_exonic"
+    - "marginal_read_through"
+    - "spliced"
+    - "hairpin"
+    - "blacklist"
+    - "min_support"
+    - "select_best"
+    - "in_vitro"
+    - "short_anchor"
+    - "known_fusions"
+    - "no_coverage"
+    - "homopolymer"
+    - "many_spliced"
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+  - type: "double"
+    name: "--max_e_value"
+    alternatives:
+    - "-E"
+    description: "Arriba estimates the number of fusions with a given number of supporting\
+      \ \nreads which one would expect to see by random chance. If the expected number\
+      \ \nof fusions (e-value) is higher than this threshold, the fusion is \ndiscarded\
+      \ by the 'relative_support' filter. Note: Increasing this \nthreshold can dramatically\
+      \ increase the number of false positives and may \nincrease the runtime of resource-intensive\
+      \ steps. Fractional values are \npossible. Default: 0.300000 \n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--min_supporting_reads"
+    alternatives:
+    - "-S"
+    description: "The 'min_support' filter discards all fusions with fewer than \n\
+      this many supporting reads (split reads and discordant mates \ncombined). Default:\
+      \ 2 \n"
+    info: null
+    example:
+    - 2
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "double"
+    name: "--max_mismappers"
+    alternatives:
+    - "-m"
+    description: "When more than this fraction of supporting reads turns out to be\
+      \ \nmismappers, the 'mismappers' filter discards the fusion. Default: \n0.800000\n"
+    info: null
+    example:
+    - 0.8
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "double"
+    name: "--max_homolog_identity"
+    alternatives:
+    - "-L"
+    description: "Genes with more than the given fraction of sequence identity are\
+      \ \nconsidered homologs and removed by the 'homologs' filter. \nDefault: 0.300000\
+      \ \n"
+    info: null
+    example:
+    - 0.3
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--homopolymer_length"
+    alternatives:
+    - "-H"
+    description: "The 'homopolymer' filter removes breakpoints adjacent to \nhomopolymers\
+      \ of the given length or more. Default: 6\n"
+    info: null
+    example:
+    - 6
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--read_through_distance"
+    alternatives:
+    - "-R"
+    description: "The 'read_through' filter removes read-through fusions \nwhere the\
+      \ breakpoints are less than the given distance away \nfrom each other. Default:\
+      \ 10000 \n"
+    info: null
+    example:
+    - 10000
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--min_anchor_length"
+    alternatives:
+    - "-A"
+    description: "Alignment artifacts are often characterized by split reads coming\
+      \ \nfrom only one gene and no discordant mates. Moreover, the split \nreads\
+      \ only align to a short stretch in one of the genes. The \n'short_anchor' filter\
+      \ removes these fusions. This parameter sets \nthe threshold in bp for what\
+      \ the filter considers short. Default: 23 \n"
+    info: null
+    example:
+    - 23
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--many_spliced_events"
+    alternatives:
+    - "-M"
+    description: "The 'many_spliced' filter recovers fusions between genes that \n\
+      have at least this many spliced breakpoints. Default: 4\n"
+    info: null
+    example:
+    - 4
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "double"
+    name: "--max_kmer_content"
+    alternatives:
+    - "-K"
+    description: "The 'low_entropy' filter removes reads with repetitive 3-mers. If\
+      \ \nthe 3-mers make up more than the given fraction of the sequence, then \n\
+      the read is discarded. Default: 0.600000 \n"
+    info: null
+    example:
+    - 0.6
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "double"
+    name: "--max_mismatch_pvalue"
+    alternatives:
+    - "-V"
+    description: "The 'mismatches' filter uses a binomial model to calculate a \n\
+      p-value for observing a given number of mismatches in a read. If \nthe number\
+      \ of mismatches is too high, the read is discarded. \nDefault: 0.010000 \n"
+    info: null
+    example:
+    - 0.05
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--fragment_length"
+    alternatives:
+    - "-F"
+    description: "When paired-end data is given, the fragment length is estimated\
+      \ \nautomatically and this parameter has no effect. But when single-end \ndata\
+      \ is given, the mean fragment length should be specified to \neffectively filter\
+      \ fusions that arise from hairpin structures. \nDefault: 200 \n"
+    info: null
+    example:
+    - 200
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--max_reads"
+    alternatives:
+    - "-U"
+    description: "Subsample fusions with more than the given number of supporting\
+      \ reads. This \nimproves performance without compromising sensitivity, as long\
+      \ as the \nthreshold is high. Counting of supporting reads beyond the threshold\
+      \ is \ninaccurate, obviously. Default: 300 \n"
+    info: null
+    example:
+    - 300
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "double"
+    name: "--quantile"
+    alternatives:
+    - "-Q"
+    description: "Highly expressed genes are prone to produce artifacts during library\
+      \ \npreparation. Genes with an expression above the given quantile are eligible\
+      \ \nfor filtering by the 'in_vitro' filter. Default: 0.998000\n"
+    info: null
+    example:
+    - 0.998
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "double"
+    name: "--exonic_fraction"
+    alternatives:
+    - "-e"
+    description: "The breakpoints of false-positive predictions of intragenic events\
+      \ \nare often both in exons. True predictions are more likely to have at \n\
+      least one breakpoint in an intron, because introns are larger. If the \nfraction\
+      \ of exonic sequence between two breakpoints is smaller than \nthe given fraction,\
+      \ the 'intragenic_exonic' filter discards the \nevent. Default: 0.330000 \n"
+    info: null
+    example:
+    - 0.33
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--top_n"
+    alternatives:
+    - "-T"
+    description: "Only report viral integration sites of the top N most highly expressed\
+      \ viral \ncontigs. Default: 5\n"
+    info: null
+    example:
+    - 5
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "double"
+    name: "--covered_fraction"
+    alternatives:
+    - "-C"
+    description: "Ignore virally associated events if the virus is not fully \nexpressed,\
+      \ i.e., less than the given fraction of the viral contig is \ntranscribed. Default:\
+      \ 0.050000 \n"
+    info: null
+    example:
+    - 0.05
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--max_itd_length"
+    alternatives:
+    - "-l"
+    description: "Maximum length of internal tandem duplications. Note: Increasing\
+      \ \nthis value beyond the default can impair performance and lead to many \n\
+      false positives. Default: 100 \n"
+    info: null
+    example:
+    - 100
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "double"
+    name: "--min_itd_allele_fraction"
+    alternatives:
+    - "-z"
+    description: "Required fraction of supporting reads to report an internal \ntandem\
+      \ duplication. Default: 0.070000 \n"
+    info: null
+    example:
+    - 0.07
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--min_itd_supporting_reads"
+    alternatives:
+    - "-Z"
+    description: "Required absolute number of supporting reads to report an \ninternal\
+      \ tandem duplication. Default: 10 \n"
+    info: null
+    example:
+    - 10
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--skip_duplicate_marking"
+    alternatives:
+    - "-u"
+    description: "Instead of performing duplicate marking itself, Arriba relies on\
+      \ duplicate marking by a \npreceding program using the BAM_FDUP flag. This makes\
+      \ sense when unique molecular \nidentifiers (UMI) are used.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--extra_information"
+    alternatives:
+    - "-X"
+    description: "To reduce the runtime and file size, by default, the columns 'fusion_transcript',\
+      \ \n'peptide_sequence', and 'read_identifiers' are left empty in the file containing\
+      \ \ndiscarded fusion candidates (see parameter -O). When this flag is set, this\
+      \ extra \ninformation is reported in the discarded fusions file.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--fill_gaps"
+    alternatives:
+    - "-I"
+    description: "If assembly of the fusion transcript sequence from the supporting\
+      \ reads is incomplete \n(denoted as '...'), fill the gaps using the assembly\
+      \ sequence wherever possible. \n"
+    info: null
+    direction: "input"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Detect gene fusions from RNA-Seq data"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test_data"
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  cpus: 1
+  commands:
+  - "ps"
+keywords:
+- "Gene fusion"
+- "RNA-Seq"
+license: "MIT"
+references:
+  doi:
+  - "10.1101/gr.257246.119"
+links:
+  repository: "https://github.com/suhrig/arriba"
+  homepage: "https://arriba.readthedocs.io/en/latest/"
+  documentation: "https://arriba.readthedocs.io/en/latest/"
+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/arriba:2.4.0--h0033a41_2"
+  target_registry: "images.viash-hub.com"
+  target_tag: "bump_viash_0_9_4"
+  namespace_separator: "/"
+  setup:
+  - type: "docker"
+    run:
+    - "arriba -h | grep 'Version:' 2>&1 |  sed 's/Version:\\s\\(.*\\)/arriba: \"\\\
+      1\"/' > /var/software_versions.txt\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/arriba/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/arriba"
+  executable: "target/executable/arriba/arriba"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/bases2fastq/.config.vsh.yaml

@@ -0,0 +1,424 @@
+name: "bases2fastq"
+version: "bump_viash_0_9_4"
+authors:
+- name: "Dries Schaumont"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "dries@data-intuitive.com"
+      github: "DriesSchaumont"
+      orcid: "0000-0002-4389-0440"
+      linkedin: "dries-schaumont"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Scientist"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--analysis_directory"
+    description: "Location of analysis directory"
+    info: null
+    example:
+    - "input"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--run_manifest"
+    alternatives:
+    - "-r"
+    description: "Location of run manifest to use instead of default RunManifest.csv\
+      \ found in analysis directory"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--output_directory"
+    alternatives:
+    - "-o"
+    description: "Location to save output fastqs"
+    info: null
+    example:
+    - "fastq_dir"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--report"
+    description: "Output location for the HTML report"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--logs"
+    description: "Directory containing log files"
+    info: null
+    example:
+    - "logs_dir"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Arguments"
+  arguments:
+  - type: "string"
+    name: "--chemistry_version"
+    description: "Run parameters override, chemistry version."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--demux_only"
+    alternatives:
+    - "-d"
+    description: "Generate demux files and indexing stats without generating FASTQ\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--detect_adapters"
+    description: "Detect adapters sequences, overriding any sequences present in run\
+      \ manifest.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--error_on_missing"
+    description: "Terminate execution for a missing file (by default, missing files\
+      \ are\nskipped and execution continues). Also set by --strict.\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--exclude_tile"
+    alternatives:
+    - "-e"
+    description: "Regex matching tile names to exclude. This flag can be specified\
+      \ multiple times. (e.g. L1.*C0[23]S.)\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+  - type: "string"
+    name: "--filter_mask"
+    description: "Run parameters override, custom pass filter mask.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--flowcell_id"
+    description: "Run parameters override, flowcell ID.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--force_index_orientation"
+    description: "Do not attempt to find orientation for I1/I2 reads (reverse complement).\n\
+      Use orientation given in run manifest.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--group_fastq"
+    description: "Group all FASTQ/stats/metrics for a project are in the project folder.\n"
+    info: null
+    direction: "input"
+  - type: "integer"
+    name: "--i1_cycles"
+    description: "Run parameters override, I1 cycles.\n"
+    info: null
+    required: false
+    min: 1
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--i2_cycles"
+    description: "Run parameters override, I2 cycles\n"
+    info: null
+    required: false
+    min: 1
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--include_tile"
+    alternatives:
+    - "-i"
+    description: "Regex matching tile names to include. This flag\ncan be specified\
+      \ multiple times. (e.g. L1.*C0[23]S.)\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+  - type: "string"
+    name: "--kit_configuration"
+    description: "Run parameters override, kit configuration.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--legacy_fastq"
+    description: "Legacy naming for FASTQ files (e.g. SampleName_S1_L001_R1_001.fastq.gz)\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--log_level"
+    alternatives:
+    - "-l"
+    description: "Severity level for logging.\n"
+    info: null
+    example:
+    - "INFO"
+    required: false
+    choices:
+    - "DEBUG"
+    - "INFO"
+    - "WARNING"
+    - "ERROR"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--no_error_on_invalid"
+    description: "Skip invalid files and continue execution. Overridden by --strict\
+      \ options\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_projects"
+    description: "Disable project directories\n"
+    info: null
+    direction: "input"
+  - type: "integer"
+    name: "--num_unassigned"
+    description: "Max Number of unassigned sequences to report.\n"
+    info: null
+    example:
+    - 30
+    required: false
+    min: 0
+    max: 1000
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--preparation_workflow"
+    description: "Run parameters override, preparation workflow. \n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--qc_only"
+    description: "Quickly generate run stats for single tile without generating FASTQ.\n\
+      Use --include_tile/--exclude_tile to define custom tile set.\n"
+    info: null
+    direction: "input"
+  - type: "integer"
+    name: "--r1_cycles"
+    description: "Run parameters override, R1 cycles.\n"
+    info: null
+    required: false
+    min: 1
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--r2_cycles"
+    description: "Run parameters override, R2 cycles.\n"
+    info: null
+    required: false
+    min: 1
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--split_lanes"
+    description: "Split FASTQ files by lane.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--strict"
+    description: "In strict mode any invalid or missing input file will terminate\
+      \ execution \n(overrides no_error_on_invalid and sets --error_on_missing)\n"
+    info: null
+    direction: "input"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Bases2Fastq demultiplexes sequencing data generated by Element Biosciences\
+  \ instruments and converts base calls into FASTQ files.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "demultiplex"
+- "fastq"
+- "demux"
+- "Element Biosciences"
+license: "Proprietairy"
+links:
+  repository: "https://github.com/viash-hub/biobox"
+  documentation: "https://docs.elembio.io/docs/bases2fastq/introduction/"
+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: "elembio/bases2fastq:2.1.0"
+  target_registry: "images.viash-hub.com"
+  target_tag: "bump_viash_0_9_4"
+  namespace_separator: "/"
+  setup:
+  - type: "apt"
+    packages:
+    - "procps"
+    - "tree"
+    interactive: false
+  - type: "docker"
+    run:
+    - "echo \"bases2fastq: $(bases2fastq --version | cut -d' ' -f3)\" > /var/software_versions.txt\n"
+  test_setup:
+  - type: "apt"
+    packages:
+    - "curl"
+    interactive: false
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/bases2fastq/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/bases2fastq"
+  executable: "target/executable/bases2fastq/bases2fastq"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/bbmap/bbmap_bbsplit/.config.vsh.yaml

@@ -0,0 +1,398 @@
+name: "bbmap_bbsplit"
+namespace: "bbmap"
+version: "bump_viash_0_9_4"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "string"
+    name: "--id"
+    description: "Sample ID"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--paired"
+    description: "Paired fastq files or not?"
+    info: null
+    direction: "input"
+  - type: "file"
+    name: "--input"
+    description: "Input fastq files, either one or two (paired), separated by \";\"\
+      ."
+    info: null
+    example:
+    - "reads.fastq"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+  - type: "file"
+    name: "--ref"
+    description: "Reference FASTA files, separated by \";\". The primary reference\
+      \ should be specified first."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--only_build_index"
+    description: "If set, only builds the index. Otherwise, mapping is performed."
+    info: null
+    direction: "input"
+  - type: "file"
+    name: "--build"
+    description: "Index to be used for mapping. \n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--qin"
+    description: "Set to 33 or 64 to specify input quality value ASCII offset. Automatically\
+      \ detected if\nnot specified.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--interleaved"
+    description: "True forces paired/interleaved input; false forces single-ended\
+      \ mapping.\nIf not specified, interleaved status will be autodetected from read\
+      \ names.\n"
+    info: null
+    direction: "input"
+  - type: "integer"
+    name: "--maxindel"
+    description: "Don't look for indels longer than this. Lower is faster. Set to\
+      \ >=100k for RNA-seq.\n"
+    info: null
+    example:
+    - 20
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "double"
+    name: "--minratio"
+    description: "Fraction of max alignment score required to keep a site. Higher\
+      \ is faster.\n"
+    info: null
+    example:
+    - 0.56
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--minhits"
+    description: "Minimum number of seed hits required for candidate sites. Higher\
+      \ is faster.\n"
+    info: null
+    example:
+    - 1
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--ambiguous"
+    description: "Set behavior on ambiguously-mapped reads (with multiple top-scoring\
+      \ mapping locations).\n  * best    Use the first best site (Default)\n  * toss\
+      \    Consider unmapped\n  * random  Select one top-scoring site randomly\n \
+      \ * all     Retain all top-scoring sites.  Does not work yet with SAM output\n"
+    info: null
+    example:
+    - "best"
+    required: false
+    choices:
+    - "best"
+    - "toss"
+    - "random"
+    - "all"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--ambiguous2"
+    description: "Set behavior only for reads that map ambiguously to multiple different\
+      \ references.\nNormal 'ambiguous=' controls behavior on all ambiguous reads;\n\
+      Ambiguous2 excludes reads that map ambiguously within a single reference.\n\
+      \  * best    Use the first best site (Default)\n  * toss    Consider unmapped\n\
+      \  * all     Write a copy to the output for each reference to which it maps\n\
+      \  * split   Write a copy to the AMBIGUOUS_ output for each reference to which\
+      \ it maps\n"
+    info: null
+    example:
+    - "best"
+    required: false
+    choices:
+    - "best"
+    - "toss"
+    - "all"
+    - "split"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--qtrim"
+    description: "Quality-trim ends to Q5 before mapping. Options are 'l' (left),\
+      \ 'r' (right), and 'lr' (both).\n"
+    info: null
+    required: false
+    choices:
+    - "l"
+    - "r"
+    - "lr"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--untrim"
+    description: "Undo trimming after mapping. Untrimmed bases will be soft-clipped\
+      \ in cigar strings."
+    info: null
+    direction: "input"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--index"
+    description: "Location to write the index.\n"
+    info: null
+    example:
+    - "BBSplit_index"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--fastq_1"
+    description: "Output file for read 1.\n"
+    info: null
+    example:
+    - "read_out1.fastq"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--fastq_2"
+    description: "Output file for read 2.\n"
+    info: null
+    example:
+    - "read_out2.fastq"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--sam2bam"
+    alternatives:
+    - "--bs"
+    description: "Write a shell script to 'file' that will turn the sam output into\
+      \ a sorted, indexed bam file.\n"
+    info: null
+    example:
+    - "script.sh"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--scafstats"
+    description: "Write statistics on how many reads mapped to which scaffold to this\
+      \ file.\n"
+    info: null
+    example:
+    - "scaffold_stats.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--refstats"
+    description: "Write statistics on how many reads were assigned to which reference\
+      \ to this file.\nUnmapped reads whose mate mapped to a reference are considered\
+      \ assigned and will be counted.\n"
+    info: null
+    example:
+    - "reference_stats.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--nzo"
+    description: "Only print lines with nonzero coverage."
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--bbmap_args"
+    description: "Additional arguments from BBMap to pass to BBSplit.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Split sequencing reads by mapping them to multiple references simultaneously."
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+license: "BBTools Copyright (c) 2014"
+links:
+  repository: "https://github.com/BioInfoTools/BBMap/blob/master/sh/bbsplit.sh"
+  homepage: "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/"
+  documentation: "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbmap-guide/"
+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: "ubuntu:22.04"
+  target_registry: "images.viash-hub.com"
+  target_tag: "bump_viash_0_9_4"
+  namespace_separator: "/"
+  setup:
+  - type: "docker"
+    run:
+    - "apt-get update && \\\napt-get install -y build-essential openjdk-17-jdk wget\
+      \ tar && \\\nwget --no-check-certificate https://sourceforge.net/projects/bbmap/files/BBMap_39.01.tar.gz\
+      \ && \\\ntar xzf BBMap_39.01.tar.gz && \\\ncp -r bbmap/* /usr/local/bin\n"
+  - type: "docker"
+    run:
+    - "bbsplit.sh --version 2>&1 | awk '/BBMap version/{print \"BBMAP:\", $NF}' >\
+      \ /var/software_versions.txt\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/bbmap/bbmap_bbsplit/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/bbmap/bbmap_bbsplit"
+  executable: "target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/bcftools/bcftools_annotate/.config.vsh.yaml

@@ -0,0 +1,499 @@
+name: "bcftools_annotate"
+namespace: "bcftools"
+version: "bump_viash_0_9_4"
+authors:
+- name: "Theodoro Gasperin Terra Camargo"
+  roles:
+  - "author"
+  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 VCF/BCF file."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    alternatives:
+    - "-o"
+    description: "Output annotated file."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Options"
+  description: "For examples on how to use use bcftools annotate see http://samtools.github.io/bcftools/howtos/annotate.html.\n\
+    For more details on the options see https://samtools.github.io/bcftools/bcftools.html#annotate.\n"
+  arguments:
+  - type: "file"
+    name: "--annotations"
+    alternatives:
+    - "--a"
+    description: "VCF file or tabix-indexed FILE with annotations: CHR\\tPOS[\\tVALUE]+\
+      \ . \n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--columns"
+    alternatives:
+    - "--c"
+    description: "List of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG.\
+      \ \nSee man page for details.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--columns_file"
+    alternatives:
+    - "--C"
+    description: "Read -c columns from FILE, one name per row, with optional --merge_logic\
+      \ TYPE: NAME[ TYPE].\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--exclude"
+    alternatives:
+    - "--e"
+    description: "Exclude sites for which the expression is true.\nSee https://samtools.github.io/bcftools/bcftools.html#expressions\
+      \ for details.\n"
+    info: null
+    example:
+    - "QUAL >= 30 && DP >= 10"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--force"
+    description: "continue even when parsing errors, such as undefined tags, are encountered.\
+      \ \nNote this can be an unsafe operation and can result in corrupted BCF files.\
+      \ \nIf this option is used, make sure to sanity check the result thoroughly.\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--header_line"
+    alternatives:
+    - "--H"
+    description: "Header line which should be appended to the VCF header, can be given\
+      \ multiple times.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--header_lines"
+    alternatives:
+    - "--h"
+    description: "File with header lines to append to the VCF header.\nFor example:\n\
+      \  ##INFO=<ID=NUMERIC_TAG,Number=1,Type=Integer,Description=\"Example header\
+      \ line\">\n  ##INFO=<ID=STRING_TAG,Number=1,Type=String,Description=\"Yet another\
+      \ header line\">\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--set_id"
+    alternatives:
+    - "--I"
+    description: "Set ID column using a `bcftools query`-like expression, see man\
+      \ page for details.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--include"
+    description: "Select sites for which the expression is true.\nSee https://samtools.github.io/bcftools/bcftools.html#expressions\
+      \ for details.\n"
+    info: null
+    example:
+    - "QUAL >= 30 && DP >= 10"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--keep_sites"
+    alternatives:
+    - "--k"
+    description: "Leave --include/--exclude sites unchanged instead of discarding\
+      \ them.\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--merge_logic"
+    alternatives:
+    - "--l"
+    description: "When multiple regions overlap a single record, this option defines\
+      \ how to treat multiple annotation values.\nSee man page for more details.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--mark_sites"
+    alternatives:
+    - "--m"
+    description: "Annotate sites which are present (\"+\") or absent (\"-\") in the\
+      \ -a file with a new INFO/TAG flag.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--min_overlap"
+    description: "Minimum overlap required as a fraction of the variant in the annotation\
+      \ -a file (ANN), \nin the target VCF file (:VCF), or both for reciprocal overlap\
+      \ (ANN:VCF). \nBy default overlaps of arbitrary length are sufficient. \nThe\
+      \ option can be used only with the tab-delimited annotation -a file and with\
+      \ BEG and END columns present.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--no_version"
+    description: "Do not append version and command line information to the output\
+      \ VCF header.\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--output_type"
+    alternatives:
+    - "--O"
+    description: "Output type:\n  u: uncompressed BCF\n  z: compressed VCF\n  b: compressed\
+      \ BCF\n  v: uncompressed VCF\n"
+    info: null
+    required: false
+    choices:
+    - "u"
+    - "z"
+    - "b"
+    - "v"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--pair_logic"
+    description: "Controls how to match records from the annotation file to the target\
+      \ VCF. \nEffective only when -a is a VCF or BCF file. \nThe option replaces\
+      \ the former uninuitive --collapse. \nSee Common Options for more.\n"
+    info: null
+    required: false
+    choices:
+    - "snps"
+    - "indels"
+    - "both"
+    - "all"
+    - "some"
+    - "exact"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--regions"
+    alternatives:
+    - "--r"
+    description: "Restrict to comma-separated list of regions. \nFollowing formats\
+      \ are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​].\n"
+    info: null
+    example:
+    - "20:1000000-2000000"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--regions_file"
+    alternatives:
+    - "--R"
+    description: "Restrict to regions listed in a file. \nRegions can be specified\
+      \ either on a VCF, BED, or tab-delimited file (the default). \nFor more information\
+      \ check manual.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--regions_overlap"
+    description: "This option controls how overlapping records are determined: \n\
+      set to 'pos' or '0' if the VCF record has to have POS inside a region (this\
+      \ corresponds to the default behavior of -t/-T); \nset to 'record' or '1' if\
+      \ also overlapping records with POS outside a region should be included (this\
+      \ is the default behavior of -r/-R, \nand includes indels with POS at the end\
+      \ of a region, which are technically outside the region); \nor set to 'variant'\
+      \ or '2' to include only true overlapping variation (compare the full VCF representation\
+      \ \"TA>T-\" vs the true sequence variation \"A>-\").\n"
+    info: null
+    required: false
+    choices:
+    - "pos"
+    - "record"
+    - "variant"
+    - "0"
+    - "1"
+    - "2"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--rename_annotations"
+    description: "Rename annotations: TYPE/old\\tnew, where TYPE is one of FILTER,INFO,FORMAT.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--rename_chromosomes"
+    description: "Rename chromosomes according to the map in file, with \"old_name\
+      \ new_name\\n\" pairs \nseparated by whitespaces, each on a separate line.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--samples"
+    description: "Subset of samples to annotate.\nSee also https://samtools.github.io/bcftools/bcftools.html#common_options.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--samples_file"
+    description: "Subset of samples to annotate in file format.\nSee also https://samtools.github.io/bcftools/bcftools.html#common_options.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--single_overlaps"
+    description: "Use this option to keep memory requirements low with very large\
+      \ annotation files. \nNote, however, that this comes at a cost, only single\
+      \ overlapping intervals are considered in this mode. \nThis was the default\
+      \ mode until the commit af6f0c9 (Feb 24 2019).\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--remove"
+    alternatives:
+    - "--x"
+    description: "List of annotations to remove. \nUse \"FILTER\" to remove all filters\
+      \ or \"FILTER/SomeFilter\" to remove a specific filter. \nSimilarly, \"INFO\"\
+      \ can be used to remove all INFO tags and \"FORMAT\" to remove all FORMAT tags\
+      \ except GT. \nTo remove all INFO tags except \"FOO\" and \"BAR\", use \"^INFO/FOO,INFO/BAR\"\
+      \ (and similarly for FORMAT and FILTER). \n\"INFO\" can be abbreviated to \"\
+      INF\" and \"FORMAT\" to \"FMT\".\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Add or remove annotations from a VCF/BCF file.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "Annotate"
+- "VCF"
+- "BCF"
+license: "MIT/Expat, GNU"
+references:
+  doi:
+  - "https://doi.org/10.1093/gigascience/giab008"
+links:
+  repository: "https://github.com/samtools/bcftools"
+  homepage: "https://samtools.github.io/bcftools/"
+  documentation: "https://samtools.github.io/bcftools/bcftools.html#annotate"
+  issue_tracker: "https://github.com/samtools/bcftools/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: "bump_viash_0_9_4"
+  namespace_separator: "/"
+  setup:
+  - type: "apt"
+    packages:
+    - "bcftools"
+    - "procps"
+    interactive: false
+  - type: "docker"
+    run:
+    - "echo \"bcftools: \\\"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools\
+      \ //p')\\\"\" > /var/software_versions.txt\n"
+  test_setup:
+  - type: "apt"
+    packages:
+    - "tabix"
+    interactive: false
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/bcftools/bcftools_annotate/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/bcftools/bcftools_annotate"
+  executable: "target/executable/bcftools/bcftools_annotate/bcftools_annotate"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/bcftools/bcftools_concat/.config.vsh.yaml

@@ -0,0 +1,365 @@
+name: "bcftools_concat"
+namespace: "bcftools"
+version: "bump_viash_0_9_4"
+authors:
+- name: "Theodoro Gasperin Terra Camargo"
+  roles:
+  - "author"
+  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 VCF/BCF files to concatenate."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+  - type: "file"
+    name: "--file_list"
+    alternatives:
+    - "-f"
+    description: "Read the list of VCF/BCF files from a file, one file name per line."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    alternatives:
+    - "-o"
+    description: "Output concatenated VCF/BCF file."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Options"
+  arguments:
+  - type: "boolean_true"
+    name: "--allow_overlaps"
+    alternatives:
+    - "-a"
+    description: "First coordinate of the next file can precede last record of the\
+      \ current file.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--compact_PS"
+    alternatives:
+    - "-c"
+    description: "Do not output PS tag at each site, only at the start of a new phase\
+      \ set block.\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--remove_duplicates"
+    alternatives:
+    - "-d"
+    description: "Output duplicate records present in multiple files only once: <snps|indels|both|all|exact>.\n\
+      \    \n"
+    info: null
+    required: false
+    choices:
+    - "snps"
+    - "indels"
+    - "both"
+    - "all"
+    - "exact"
+    - "none"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--ligate"
+    alternatives:
+    - "-l"
+    description: "Ligate phased VCFs by matching phase at overlapping haplotypes."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--ligate_force"
+    description: "Ligate even non-overlapping chunks, keep all sites."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--ligate_warn"
+    description: "Drop sites in imperfect overlaps."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_version"
+    description: "Do not append version and command line information to the header."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--naive"
+    alternatives:
+    - "-n"
+    description: "Concatenate files without recompression, a header check compatibility\
+      \ is performed."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--naive_force"
+    description: "Same as --naive, but header compatibility is not checked. \nDangerous,\
+      \ use with caution.\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--output_type"
+    alternatives:
+    - "-O"
+    description: "Output type:\n  u: uncompressed BCF\n  z: compressed VCF\n  b: compressed\
+      \ BCF\n  v: uncompressed VCF\n"
+    info: null
+    required: false
+    choices:
+    - "u"
+    - "z"
+    - "b"
+    - "v"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--min_PQ"
+    alternatives:
+    - "-q"
+    description: "Break phase set if phasing quality is lower than <int>."
+    info: null
+    example:
+    - 30
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--regions"
+    alternatives:
+    - "-r"
+    description: "Restrict to comma-separated list of regions. \nFollowing formats\
+      \ are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​].\n"
+    info: null
+    example:
+    - "20:1000000-2000000"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--regions_file"
+    alternatives:
+    - "-R"
+    description: "Restrict to regions listed in a file. \nRegions can be specified\
+      \ either on a VCF, BED, or tab-delimited file (the default). \nFor more information\
+      \ check manual.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--regions_overlap"
+    description: "This option controls how overlapping records are determined: \n\
+      set to 'pos' or '0' if the VCF record has to have POS inside a region (this\
+      \ corresponds to the default behavior of -t/-T); \nset to 'record' or '1' if\
+      \ also overlapping records with POS outside a region should be included (this\
+      \ is the default behavior of -r/-R, \nand includes indels with POS at the end\
+      \ of a region, which are technically outside the region); \nor set to 'variant'\
+      \ or '2' to include only true overlapping variation (compare the full VCF representation\
+      \ \"TA>T-\" vs the true sequence variation \"A>-\").\n"
+    info: null
+    required: false
+    choices:
+    - "pos"
+    - "record"
+    - "variant"
+    - "0"
+    - "1"
+    - "2"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Concatenate or combine VCF/BCF files. All source files must have the\
+  \ same sample\ncolumns appearing in the same order. The program can be used, for\
+  \ example, to\nconcatenate chromosome VCFs into one VCF, or combine a SNP VCF and\
+  \ an indel\nVCF into one. The input files must be sorted by chr and position. The\
+  \ files\nmust be given in the correct order to produce sorted VCF on output unless\n\
+  the -a, --allow-overlaps option is specified. With the --naive option, the files\n\
+  are concatenated without being recompressed, which is very fast.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "Concatenate"
+- "VCF"
+- "BCF"
+license: "MIT/Expat, GNU"
+references:
+  doi:
+  - "https://doi.org/10.1093/gigascience/giab008"
+links:
+  repository: "https://github.com/samtools/bcftools"
+  homepage: "https://samtools.github.io/bcftools/"
+  documentation: "https://samtools.github.io/bcftools/bcftools.html#concat"
+  issue_tracker: "https://github.com/samtools/bcftools/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: "bump_viash_0_9_4"
+  namespace_separator: "/"
+  setup:
+  - type: "apt"
+    packages:
+    - "bcftools"
+    - "procps"
+    interactive: false
+  - type: "docker"
+    run:
+    - "echo \"bcftools: \\\"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools\
+      \ //p')\\\"\" > /var/software_versions.txt\n"
+  test_setup:
+  - type: "apt"
+    packages:
+    - "tabix"
+    interactive: false
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/bcftools/bcftools_concat/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/bcftools/bcftools_concat"
+  executable: "target/executable/bcftools/bcftools_concat/bcftools_concat"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/bcftools/bcftools_norm/.config.vsh.yaml

@@ -0,0 +1,446 @@
+name: "bcftools_norm"
+namespace: "bcftools"
+version: "bump_viash_0_9_4"
+authors:
+- name: "Theodoro Gasperin Terra Camargo"
+  roles:
+  - "author"
+  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 VCF/BCF 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 normalized VCF/BCF file."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Options"
+  arguments:
+  - type: "boolean_true"
+    name: "--atomize"
+    alternatives:
+    - "-a"
+    description: "Decompose complex variants (e.g., MNVs become consecutive SNVs).\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--atom_overlaps"
+    description: "Use the star allele (*) for overlapping alleles or set to missing\
+      \ (.).\n"
+    info: null
+    required: false
+    choices:
+    - "."
+    - "*"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--check_ref"
+    alternatives:
+    - "-c"
+    description: "Check REF alleles and exit (e), warn (w), exclude (x), or set (s)\
+      \ bad sites.\n"
+    info: null
+    required: false
+    choices:
+    - "e"
+    - "w"
+    - "x"
+    - "s"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--remove_duplicates"
+    alternatives:
+    - "-d"
+    description: "Remove duplicate snps, indels, both, all, exact matches, or none\
+      \ (old -D option)."
+    info: null
+    required: false
+    choices:
+    - "snps"
+    - "indels"
+    - "both"
+    - "all"
+    - "exact"
+    - "none"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--fasta_ref"
+    alternatives:
+    - "-f"
+    description: "Reference fasta sequence file."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--force"
+    description: "Try to proceed even if malformed tags are encountered. \nExperimental,\
+      \ use at your own risk.\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--keep_sum"
+    description: "Keep vector sum constant when splitting multiallelics (see github\
+      \ issue #360).\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--multiallelics"
+    alternatives:
+    - "-m"
+    description: "Split multiallelics (-) or join biallelics (+), type: snps, indels,\
+      \ both, any [default: both].\n"
+    info: null
+    required: false
+    choices:
+    - "+snps"
+    - "+indels"
+    - "+both"
+    - "+any"
+    - "-snps"
+    - "-indels"
+    - "-both"
+    - "-any"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--no_version"
+    description: "Do not append version and command line information to the header."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--do_not_normalize"
+    alternatives:
+    - "-N"
+    description: "Do not normalize indels (with -m or -c s)."
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--output_type"
+    alternatives:
+    - "--O"
+    description: "Output type:\n  u: uncompressed BCF\n  z: compressed VCF\n  b: compressed\
+      \ BCF\n  v: uncompressed VCF\n"
+    info: null
+    required: false
+    choices:
+    - "u"
+    - "z"
+    - "b"
+    - "v"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--old_rec_tag"
+    description: "Annotate modified records with INFO/STR indicating the original\
+      \ variant."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--regions"
+    alternatives:
+    - "--r"
+    description: "Restrict to comma-separated list of regions. \nFollowing formats\
+      \ are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​].\n"
+    info: null
+    example:
+    - "20:1000000-2000000"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--regions_file"
+    alternatives:
+    - "--R"
+    description: "Restrict to regions listed in a file. \nRegions can be specified\
+      \ either on a VCF, BED, or tab-delimited file (the default). \nFor more information\
+      \ check manual.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--regions_overlap"
+    description: "This option controls how overlapping records are determined: \n\
+      set to 'pos' or '0' if the VCF record has to have POS inside a region (this\
+      \ corresponds to the default behavior of -t/-T); \nset to 'record' or '1' if\
+      \ also overlapping records with POS outside a region should be included (this\
+      \ is the default behavior of -r/-R, \nand includes indels with POS at the end\
+      \ of a region, which are technically outside the region); \nor set to 'variant'\
+      \ or '2' to include only true overlapping variation (compare the full VCF representation\
+      \ \"TA>T-\" vs the true sequence variation \"A>-\").\n"
+    info: null
+    required: false
+    choices:
+    - "pos"
+    - "record"
+    - "variant"
+    - "0"
+    - "1"
+    - "2"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--site_win"
+    alternatives:
+    - "-w"
+    description: "Buffer for sorting lines that changed position during realignment.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--strict_filter"
+    alternatives:
+    - "-s"
+    description: "When merging (-m+), merged site is PASS only if all sites being\
+      \ merged PASS."
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--targets"
+    alternatives:
+    - "-t"
+    description: "Similar to --regions but streams rather than index-jumps."
+    info: null
+    example:
+    - "20:1000000-2000000"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--targets_file"
+    alternatives:
+    - "-T"
+    description: "Similar to --regions_file but streams rather than index-jumps."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--targets_overlap"
+    description: "Include if POS in the region (0), record overlaps (1), variant overlaps\
+      \ (2).\nSimilar to --regions_overlap.\n"
+    info: null
+    required: false
+    choices:
+    - "pos"
+    - "record"
+    - "variant"
+    - "0"
+    - "1"
+    - "2"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Left-align and normalize indels, check if REF alleles match the reference,\
+  \ split multiallelic sites into multiple rows; \nrecover multiallelics from multiple\
+  \ rows. \n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "Normalize"
+- "VCF"
+- "BCF"
+license: "MIT/Expat, GNU"
+references:
+  doi:
+  - "https://doi.org/10.1093/gigascience/giab008"
+links:
+  repository: "https://github.com/samtools/bcftools"
+  homepage: "https://samtools.github.io/bcftools/"
+  documentation: "https://samtools.github.io/bcftools/bcftools.html#norm"
+  issue_tracker: "https://github.com/samtools/bcftools/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: "bump_viash_0_9_4"
+  namespace_separator: "/"
+  setup:
+  - type: "apt"
+    packages:
+    - "bcftools"
+    - "procps"
+    interactive: false
+  - type: "docker"
+    run:
+    - "echo \"bcftools: \\\"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools\
+      \ //p')\\\"\" > /var/software_versions.txt\n"
+  test_setup:
+  - type: "apt"
+    packages:
+    - "tabix"
+    interactive: false
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/bcftools/bcftools_norm/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/bcftools/bcftools_norm"
+  executable: "target/executable/bcftools/bcftools_norm/bcftools_norm"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/bcftools/bcftools_sort/.config.vsh.yaml

@@ -0,0 +1,215 @@
+name: "bcftools_sort"
+namespace: "bcftools"
+version: "bump_viash_0_9_4"
+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 VCF/BCF 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 sorted VCF/BCF file."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Options"
+  arguments:
+  - type: "string"
+    name: "--output_type"
+    alternatives:
+    - "-O"
+    description: "Compresses or uncompresses the output.\nThe options are:\n  b: compressed\
+      \ BCF, \n  u: uncompressed BCF, \n  z: compressed VCF, \n  v: uncompressed VCF.\
+      \        \n"
+    info: null
+    required: false
+    choices:
+    - "b"
+    - "u"
+    - "z"
+    - "v"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Sorts VCF/BCF files.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test_data"
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "Sort"
+- "VCF"
+- "BCF"
+license: "MIT/Expat, GNU"
+references:
+  doi:
+  - "https://doi.org/10.1093/gigascience/giab008"
+links:
+  repository: "https://github.com/samtools/bcftools"
+  homepage: "https://samtools.github.io/bcftools/"
+  documentation: "https://samtools.github.io/bcftools/bcftools.html#sort"
+  issue_tracker: "https://github.com/samtools/bcftools/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: "bump_viash_0_9_4"
+  namespace_separator: "/"
+  setup:
+  - type: "apt"
+    packages:
+    - "bcftools"
+    - "procps"
+    interactive: false
+  - type: "docker"
+    run:
+    - "echo \"bcftools: \\\"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools\
+      \ //p')\\\"\" > /var/software_versions.txt\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/bcftools/bcftools_sort/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/bcftools/bcftools_sort"
+  executable: "target/executable/bcftools/bcftools_sort/bcftools_sort"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/bcftools/bcftools_stats/.config.vsh.yaml

@@ -0,0 +1,488 @@
+name: "bcftools_stats"
+namespace: "bcftools"
+version: "bump_viash_0_9_4"
+authors:
+- name: "Theodoro Gasperin Terra Camargo"
+  roles:
+  - "author"
+  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 VCF/BCF file. Maximum of two files."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    alternatives:
+    - "-o"
+    description: "Output txt statistics file."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Options"
+  arguments:
+  - type: "string"
+    name: "--allele_frequency_bins"
+    alternatives:
+    - "--af_bins"
+    description: "Allele frequency bins, a list of bin values (0.1,0.5,1).\n"
+    info: null
+    example:
+    - "0.1,0.5,1"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--allele_frequency_bins_file"
+    alternatives:
+    - "--af_bins_file"
+    description: "Same as allele_frequency_bins, but in a file.\nFormat of file is\
+      \ one value per line. \ne.g. \n  0.1\n  0.5\n  1\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--allele_frequency_tag"
+    alternatives:
+    - "--af_tag"
+    description: "Allele frequency tag to use, by default estimated from AN,AC or\
+      \ GT.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--first_allele_only"
+    alternatives:
+    - "--first_only"
+    description: "Include only 1st allele at multiallelic sites.\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--collapse"
+    alternatives:
+    - "--c"
+    description: "Treat as identical records with <snps|indels|both|all|some|none>.\n\
+      See https://samtools.github.io/bcftools/bcftools.html#common_options for details.\n"
+    info: null
+    required: false
+    choices:
+    - "snps"
+    - "indels"
+    - "both"
+    - "all"
+    - "some"
+    - "none"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--depth"
+    alternatives:
+    - "--d"
+    description: "Depth distribution: min,max,bin size.\n"
+    info: null
+    example:
+    - "0,500,1"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--exclude"
+    alternatives:
+    - "--e"
+    description: "Exclude sites for which the expression is true.\nSee https://samtools.github.io/bcftools/bcftools.html#expressions\
+      \ for details.\n"
+    info: null
+    example:
+    - "QUAL < 30 && DP < 10"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--exons"
+    alternatives:
+    - "--E"
+    description: "tab-delimited file with exons for indel frameshifts statistics.\
+      \ \nThe columns of the file are CHR, FROM, TO, with 1-based, inclusive, positions.\
+      \ \nThe file is BGZF-compressed and indexed with tabix (e.g. tabix -s1 -b2 -e3\
+      \ file.gz).\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--apply_filters"
+    alternatives:
+    - "--f"
+    description: "Require at least one of the listed FILTER strings (e.g. \"PASS,.\"\
+      ).\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--fasta_reference"
+    alternatives:
+    - "--F"
+    description: "Faidx indexed reference sequence file to determine INDEL context.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--include"
+    alternatives:
+    - "--i"
+    description: "Select sites for which the expression is true.\nSee https://samtools.github.io/bcftools/bcftools.html#expressions\
+      \ for details.\n"
+    info: null
+    example:
+    - "QUAL >= 30 && DP >= 10"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--split_by_ID"
+    alternatives:
+    - "--I"
+    description: "Collect stats for sites with ID separately (known vs novel).\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--regions"
+    alternatives:
+    - "--r"
+    description: "Restrict to comma-separated list of regions. \nFollowing formats\
+      \ are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​].\n"
+    info: null
+    example:
+    - "20:1000000-2000000"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--regions_file"
+    alternatives:
+    - "--R"
+    description: "Restrict to regions listed in a file. \nRegions can be specified\
+      \ either on a VCF, BED, or tab-delimited file (the default). \nFor more information\
+      \ check manual.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--regions_overlap"
+    description: "This option controls how overlapping records are determined: \n\
+      set to 'pos' or '0' if the VCF record has to have POS inside a region (this\
+      \ corresponds to the default behavior of -t/-T); \nset to 'record' or '1' if\
+      \ also overlapping records with POS outside a region should be included (this\
+      \ is the default behavior of -r/-R, \nand includes indels with POS at the end\
+      \ of a region, which are technically outside the region); \nor set to 'variant'\
+      \ or '2' to include only true overlapping variation (compare the full VCF representation\
+      \ \"TA>T-\" vs the true sequence variation \"A>-\").\n"
+    info: null
+    required: false
+    choices:
+    - "pos"
+    - "record"
+    - "variant"
+    - "0"
+    - "1"
+    - "2"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--samples"
+    alternatives:
+    - "--s"
+    description: "List of samples for sample stats, \"-\" to include all samples.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--samples_file"
+    alternatives:
+    - "--S"
+    description: "File of samples to include.\ne.g. \n  sample1    1\n  sample2  \
+      \  2\n  sample3    2\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--targets"
+    alternatives:
+    - "--t"
+    description: "Similar as -r, --regions, but the next position is accessed by streaming\
+      \ the whole VCF/BCF \nrather than using the tbi/csi index. Both -r and -t options\
+      \ can be applied simultaneously: -r uses the \nindex to jump to a region and\
+      \ -t discards positions which are not in the targets. Unlike -r, targets \n\
+      can be prefixed with \"^\" to request logical complement. For example, \"^X,Y,MT\"\
+      \ indicates that \nsequences X, Y and MT should be skipped. Yet another difference\
+      \ between the -t/-T and -r/-R is \nthat -r/-R checks for proper overlaps and\
+      \ considers both POS and the end position of an indel, \nwhile -t/-T considers\
+      \ the POS coordinate only (by default; see also --regions-overlap and --targets-overlap).\
+      \ \nNote that -t cannot be used in combination with -T.\nFollowing formats are\
+      \ supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​].\n"
+    info: null
+    example:
+    - "20:1000000-2000000"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--targets_file"
+    alternatives:
+    - "--T"
+    description: "Similar to --regions_file option but streams rather than index-jumps.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--targets_overlaps"
+    description: "Include if POS in the region (0), record overlaps (1), variant overlaps\
+      \ (2).\n"
+    info: null
+    required: false
+    choices:
+    - "pos"
+    - "record"
+    - "variant"
+    - "0"
+    - "1"
+    - "2"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--user_tstv"
+    alternatives:
+    - "--u"
+    description: "Collect Ts/Tv stats for any tag using the given binning [0:1:100].\n\
+      Format is <TAG[:min:max:n]>.\nA subfield can be selected as e.g. 'PV4[0]', here\
+      \ the first value of the PV4 tag.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--verbose"
+    alternatives:
+    - "--v"
+    description: "Produce verbose per-site and per-sample output.\n"
+    info: null
+    direction: "input"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Parses VCF or BCF and produces a txt stats file which can be plotted\
+  \ using plot-vcfstats.\nWhen two files are given, the program generates separate\
+  \ stats for intersection\nand the complements. By default only sites are compared,\
+  \ -s/-S must given to include\nalso sample columns.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "Stats"
+- "VCF"
+- "BCF"
+license: "MIT/Expat, GNU"
+references:
+  doi:
+  - "https://doi.org/10.1093/gigascience/giab008"
+links:
+  repository: "https://github.com/samtools/bcftools"
+  homepage: "https://samtools.github.io/bcftools/"
+  documentation: "https://samtools.github.io/bcftools/bcftools.html#stats"
+  issue_tracker: "https://github.com/samtools/bcftools/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: "bump_viash_0_9_4"
+  namespace_separator: "/"
+  setup:
+  - type: "apt"
+    packages:
+    - "bcftools"
+    - "procps"
+    interactive: false
+  - type: "docker"
+    run:
+    - "echo \"bcftools: \\\"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools\
+      \ //p')\\\"\" > /var/software_versions.txt\n"
+  test_setup:
+  - type: "apt"
+    packages:
+    - "tabix"
+    interactive: false
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/bcftools/bcftools_stats/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/bcftools/bcftools_stats"
+  executable: "target/executable/bcftools/bcftools_stats/bcftools_stats"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/bcl_convert/.config.vsh.yaml

@@ -0,0 +1,458 @@
+name: "bcl_convert"
+version: "bump_viash_0_9_4"
+authors:
+- name: "Toni Verbeiren"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      github: "tverbeiren"
+      linkedin: "verbeiren"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Scientist and CEO"
+- name: "Dorien Roosen"
+  roles:
+  - "author"
+  info:
+    links:
+      email: "dorien@data-intuitive.com"
+      github: "dorien-er"
+      linkedin: "dorien-roosen"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Scientist"
+argument_groups:
+- name: "Input arguments"
+  arguments:
+  - type: "file"
+    name: "--bcl_input_directory"
+    alternatives:
+    - "-i"
+    description: "Input run directory"
+    info: null
+    example:
+    - "bcl_dir"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--sample_sheet"
+    alternatives:
+    - "-s"
+    description: "Path to SampleSheet.csv file (default searched for in --bcl_input_directory)"
+    info: null
+    example:
+    - "bcl_dir/sample_sheet.csv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--run_info"
+    description: "Path to RunInfo.xml file (default root of BCL input directory)"
+    info: null
+    example:
+    - "bcl_dir/RunInfo.xml"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Lane and tile settings"
+  arguments:
+  - type: "integer"
+    name: "--bcl_only_lane"
+    description: "Convert only specified lane number (default all lanes)"
+    info: null
+    example:
+    - 1
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--first_tile_only"
+    description: "Only convert first tile of input (for testing & debugging)"
+    info: null
+    example:
+    - true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--tiles"
+    description: "Process only a subset of tiles by a regular expression"
+    info: null
+    example:
+    - "s_[0-9]+_1"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--exclude_tiles"
+    description: "Exclude set of tiles by a regular expression"
+    info: null
+    example:
+    - "s_[0-9]+_1"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Resource arguments"
+  arguments:
+  - type: "boolean"
+    name: "--shared_thread_odirect_output"
+    description: "Use linux native asynchronous io (io_submit) for file output (Default=false)"
+    info: null
+    example:
+    - true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--bcl_num_parallel_tiles"
+    description: "\\# of tiles to process in parallel (default 1)"
+    info: null
+    example:
+    - 1
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--bcl_num_conversion_threads"
+    description: "\\# of threads for conversion (per tile, default # cpu threads)"
+    info: null
+    example:
+    - 1
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--bcl_num_compression_threads"
+    description: "\\# of threads for fastq.gz output compression (per tile, default\
+      \ # cpu threads, or HW+12)"
+    info: null
+    example:
+    - 1
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--bcl_num_decompression_threads"
+    description: "\\# of threads for bcl/cbcl input decompression (per tile, default\
+      \ half # cpu threads, or HW+8). Only applies when preloading files"
+    info: null
+    example:
+    - 1
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Run arguments"
+  arguments:
+  - type: "boolean"
+    name: "--bcl_only_matched_reads"
+    description: "For pure BCL conversion, do not output files for 'Undetermined'\
+      \ [unmatched] reads (output by default)"
+    info: null
+    example:
+    - true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--no_lane_splitting"
+    description: "Do not split FASTQ file by lane (false by default)"
+    info: null
+    example:
+    - true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--num_unknown_barcodes_reported"
+    description: "\\# of Top Unknown Barcodes to output (1000 by default)"
+    info: null
+    example:
+    - 1000
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--bcl_validate_sample_sheet_only"
+    description: "Only validate RunInfo.xml & SampleSheet files (produce no FASTQ\
+      \ files)"
+    info: null
+    example:
+    - true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--strict_mode"
+    description: "Abort if any files are missing (false by default)"
+    info: null
+    example:
+    - true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--sample_name_column_enabled"
+    description: "Use sample sheet 'Sample_Name' column when naming fastq files &\
+      \ subdirectories"
+    info: null
+    example:
+    - true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output arguments"
+  arguments:
+  - type: "file"
+    name: "--output_directory"
+    alternatives:
+    - "-o"
+    description: "Output directory containig fastq files"
+    info: null
+    example:
+    - "fastq_dir"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--bcl_sampleproject_subdirectories"
+    description: "Output to subdirectories based upon sample sheet 'Sample_Project'\
+      \ column"
+    info: null
+    example:
+    - true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--fastq_gzip_compression_level"
+    description: "Set fastq output compression level 0-9 (default 1)"
+    info: null
+    example:
+    - 1
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--reports"
+    description: "Reports directory"
+    info: null
+    example:
+    - "reports_dir"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--logs"
+    description: "Reports directory"
+    info: null
+    example:
+    - "logs_dir"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--force"
+    description: "Allow destination directory to already exist and overwrite files.\n"
+    info: null
+    example:
+    - true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Convert bcl files to fastq files using bcl-convert.\nInformation about\
+  \ upgrading from bcl2fastq via\n[Upgrading from bcl2fastq to BCL Convert](https://emea.support.illumina.com/bulletins/2020/10/upgrading-from-bcl2fastq-to-bcl-convert.html)\n\
+  and [BCL Convert Compatible Products](https://support.illumina.com/sequencing/sequencing_software/bcl-convert/compatibility.html)\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "demultiplex"
+- "fastq"
+- "bcl"
+- "illumina"
+license: "Proprietary"
+links:
+  repository: "https://github.com/viash-hub/biobox"
+  homepage: "https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html"
+  documentation: "https://support.illumina.com/downloads/bcl-convert-user-guide.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:trixie-slim"
+  target_registry: "images.viash-hub.com"
+  target_tag: "bump_viash_0_9_4"
+  namespace_separator: "/"
+  setup:
+  - type: "apt"
+    packages:
+    - "wget"
+    - "gdb"
+    - "which"
+    - "hostname"
+    - "alien"
+    - "procps"
+    interactive: false
+  - type: "docker"
+    run:
+    - "wget https://s3.amazonaws.com/webdata.illumina.com/downloads/software/bcl-convert/bcl-convert-4.2.7-2.el8.x86_64.rpm\
+      \ -O /tmp/bcl-convert.rpm && \\\nalien -i /tmp/bcl-convert.rpm && \\\nrm -rf\
+      \ /var/lib/apt/lists/* && \\\nrm /tmp/bcl-convert.rpm\n"
+  - type: "docker"
+    run:
+    - "echo \"bcl-convert: \\\"$(bcl-convert -V 2>&1 >/dev/null | sed -n '/Version/\
+      \ s/^bcl-convert\\ Version //p')\\\"\" > /var/software_versions.txt\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/bcl_convert/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/bcl_convert"
+  executable: "target/executable/bcl_convert/bcl_convert"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml

@@ -0,0 +1,304 @@
+name: "bd_rhapsody_make_reference"
+namespace: "bd_rhapsody"
+version: "bump_viash_0_9_4"
+authors:
+- name: "Robrecht Cannoodt"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "robrecht@data-intuitive.com"
+      github: "rcannood"
+      orcid: "0000-0003-3641-729X"
+      linkedin: "robrechtcannoodt"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Science Engineer"
+    - name: "Open Problems"
+      href: "https://openproblems.bio"
+      role: "Core Member"
+- name: "Weiwei Schultz"
+  roles:
+  - "contributor"
+  info:
+    organizations:
+    - name: "Janssen R&D US"
+      role: "Associate Director Data Sciences"
+argument_groups:
+- name: "Inputs"
+  arguments:
+  - type: "file"
+    name: "--genome_fasta"
+    description: "Reference genome file in FASTA or FASTA.GZ format. The BD Rhapsody\
+      \ Sequencing Analysis Pipeline uses GRCh38 for Human and GRCm39 for Mouse."
+    info:
+      config_key: "Genome_fasta"
+    example:
+    - "genome_sequence.fa.gz"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+  - type: "file"
+    name: "--gtf"
+    description: "File path to the transcript annotation files in GTF or GTF.GZ format.\
+      \ The Sequence Analysis Pipeline requires the 'gene_name' or \n'gene_id' attribute\
+      \ to be set on each gene and exon feature. Gene and exon feature lines must\
+      \ have the same attribute, and exons\nmust have a corresponding gene with the\
+      \ same value. For TCR/BCR assays, the TCR or BCR gene segments must have the\
+      \ 'gene_type' or\n'gene_biotype' attribute set, and the value should begin with\
+      \ 'TR' or 'IG', respectively.\n"
+    info:
+      config_key: "Gtf"
+    example:
+    - "transcriptome_annotation.gtf.gz"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+  - type: "file"
+    name: "--extra_sequences"
+    description: "File path to additional sequences in FASTA format to use when building\
+      \ the STAR index. (e.g. transgenes or CRISPR guide barcodes).\nGTF lines for\
+      \ these sequences will be automatically generated and combined with the main\
+      \ GTF.\n"
+    info:
+      config_key: "Extra_sequences"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--reference_archive"
+    description: "A Compressed archive containing the Reference Genome Index and annotation\
+      \ GTF files. This archive is meant to be used as an\ninput in the BD Rhapsody\
+      \ Sequencing Analysis Pipeline.\n"
+    info: null
+    example:
+    - "star_index.tar.gz"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Arguments"
+  arguments:
+  - type: "string"
+    name: "--mitochondrial_contigs"
+    description: "Names of the Mitochondrial contigs in the provided Reference Genome.\
+      \ Fragments originating from contigs other than these are\nidentified as 'nuclear\
+      \ fragments' in the ATACseq analysis pipeline.\n"
+    info:
+      config_key: "Mitochondrial_contigs"
+    default:
+    - "chrM"
+    - "chrMT"
+    - "M"
+    - "MT"
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--filtering_off"
+    description: "By default the input Transcript Annotation files are filtered based\
+      \ on the gene_type/gene_biotype attribute. Only features \nhaving the following\
+      \ attribute values are kept:\n\n  - protein_coding\n  - lncRNA (lincRNA and\
+      \ antisense for Gencode < v31/M22/Ensembl97)\n  - IG_LV_gene\n  - IG_V_gene\n\
+      \  - IG_V_pseudogene\n  - IG_D_gene\n  - IG_J_gene\n  - IG_J_pseudogene\n  -\
+      \ IG_C_gene\n  - IG_C_pseudogene\n  - TR_V_gene\n  - TR_V_pseudogene\n  - TR_D_gene\n\
+      \  - TR_J_gene\n  - TR_J_pseudogene\n  - TR_C_gene\n\n  If you have already\
+      \ pre-filtered the input Annotation files and/or wish to turn-off the filtering,\
+      \ please set this option to True.\n"
+    info:
+      config_key: "Filtering_off"
+    direction: "input"
+  - type: "boolean_true"
+    name: "--wta_only_index"
+    description: "Build a WTA only index, otherwise builds a WTA + ATAC index."
+    info:
+      config_key: "Wta_Only"
+    direction: "input"
+  - type: "string"
+    name: "--extra_star_params"
+    description: "Additional parameters to pass to STAR when building the genome index.\
+      \ Specify exactly like how you would on the command line."
+    info:
+      config_key: "Extra_STAR_params"
+    example:
+    - "--limitGenomeGenerateRAM 48000 --genomeSAindexNbases 11"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "python_script"
+  path: "script.py"
+  is_executable: true
+description: "The Reference Files Generator creates an archive containing Genome Index\n\
+  and Transcriptome annotation files needed for the BD Rhapsody Sequencing\nAnalysis\
+  \ Pipeline. The app takes as input one or more FASTA and GTF files\nand produces\
+  \ a compressed archive in the form of a tar.gz file. The \narchive contains:\n\n\
+  - STAR index\n- Filtered GTF file\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test_data"
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "genome"
+- "reference"
+- "index"
+- "align"
+license: "Unknown"
+links:
+  repository: "https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1/Extra_Utilities/"
+  documentation: "https://bd-rhapsody-bioinfo-docs.genomics.bd.com/resources/extra_utilities.html#make-rhapsody-reference"
+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: "bdgenomics/rhapsody:2.2.1"
+  target_registry: "images.viash-hub.com"
+  target_tag: "bump_viash_0_9_4"
+  namespace_separator: "/"
+  setup:
+  - type: "apt"
+    packages:
+    - "procps"
+    - "git"
+    interactive: false
+  - type: "python"
+    user: false
+    packages:
+    - "cwlref-runner"
+    - "cwl-runner"
+    upgrade: true
+  - type: "docker"
+    run:
+    - "mkdir /var/bd_rhapsody_cwl && \\\n  cd /var/bd_rhapsody_cwl && \\\n  git clone\
+      \ https://bitbucket.org/CRSwDev/cwl.git . && \\\n  git checkout 8feeace1141b24749ea6003f8e6ad6d3ad5232de\n"
+  - type: "docker"
+    run:
+    - "VERSION=$(ls -v /var/bd_rhapsody_cwl | grep '^v' | sed 's#v##' | tail -1)"
+    - "echo \"bdgenomics/rhapsody: \\\"$VERSION\\\"\" > /var/software_versions.txt"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/bd_rhapsody/bd_rhapsody_make_reference/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/bd_rhapsody/bd_rhapsody_make_reference"
+  executable: "target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/bedtools/bedtools_bamtobed/.config.vsh.yaml

@@ -0,0 +1,265 @@
+name: "bedtools_bamtobed"
+namespace: "bedtools"
+version: "bump_viash_0_9_4"
+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"
+scope:
+  image: "public"
+  target: "public"
+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: "bump_viash_0_9_4"
+  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: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml

@@ -0,0 +1,217 @@
+name: "bedtools_bamtofastq"
+namespace: "bedtools"
+version: "bump_viash_0_9_4"
+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 to be converted to FASTQ."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--fastq"
+    alternatives:
+    - "-fq"
+    description: "Output FASTQ file."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--fastq2"
+    alternatives:
+    - "-fq2"
+    description: "FASTQ for second end. Used if BAM contains paired-end data.\nBAM\
+      \ should be sorted by query name is creating paired FASTQ.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Options"
+  arguments:
+  - type: "boolean_true"
+    name: "--tags"
+    description: "Create FASTQ based on the mate info in the BAM R2 and Q2 tags.\n"
+    info: null
+    direction: "input"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Conversion tool for extracting FASTQ records from sequence alignments\
+  \ in BAM format.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test_data"
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "Conversion"
+- "BAM"
+- "FASTQ"
+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/bamtofastq.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: "bump_viash_0_9_4"
+  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_bamtofastq/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/bedtools/bedtools_bamtofastq"
+  executable: "target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml

@@ -0,0 +1,206 @@
+name: "bedtools_bed12tobed6"
+namespace: "bedtools"
+version: "bump_viash_0_9_4"
+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 BED12 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 BED6 file to be written."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Options"
+  arguments:
+  - type: "boolean_true"
+    name: "--n_score"
+    alternatives:
+    - "-n"
+    description: "Force the score to be the (1-based) block number from the BED12.\n"
+    info: null
+    direction: "input"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Converts BED features in BED12 (a.k.a. “blocked” BED features such as\
+  \ genes) to discrete BED6 features.\nFor example, in the case of a gene with six\
+  \ exons, bed12ToBed6 would create six separate BED6 features (i.e., one for each\
+  \ exon).\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "Converts"
+- "BED12"
+- "BED6"
+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/bed12tobed6.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: "bump_viash_0_9_4"
+  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_bed12tobed6/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/bedtools/bedtools_bed12tobed6"
+  executable: "target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml

@@ -0,0 +1,244 @@
+name: "bedtools_bedtobam"
+namespace: "bedtools"
+version: "bump_viash_0_9_4"
+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 file (bed/gff/vcf)."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--genome"
+    alternatives:
+    - "-g"
+    description: "Input genome file.\nNOTE: This is not a fasta file. This is a two-column\
+      \ tab-delimited file\nwhere the first column is the chromosome name and the\
+      \ second their sizes.\n"
+    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 BAM file to be written."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Options"
+  arguments:
+  - type: "integer"
+    name: "--map_quality"
+    alternatives:
+    - "-mapq"
+    description: "Set the mappinq quality for the BAM records.\n"
+    info: null
+    default:
+    - 255
+    required: false
+    min: 0
+    max: 255
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--bed12"
+    description: "The BED file is in BED12 format. The BAM CIGAR\nstring will reflect\
+      \ BED \"blocks\".\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--uncompress_bam"
+    alternatives:
+    - "-ubam"
+    description: "Write uncompressed BAM output. Default writes compressed BAM.\n"
+    info: null
+    direction: "input"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Converts feature records (bed/gff/vcf) to BAM format."
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "Converts"
+- "BED"
+- "GFF"
+- "VCF"
+- "BAM"
+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/bedtobam.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: "bump_viash_0_9_4"
+  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"
+  test_setup:
+  - type: "apt"
+    packages:
+    - "samtools"
+    interactive: false
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/bedtools/bedtools_bedtobam/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/bedtools/bedtools_bedtobam"
+  executable: "target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml

@@ -0,0 +1,367 @@
+name: "bedtools_genomecov"
+namespace: "bedtools"
+version: "bump_viash_0_9_4"
+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: "The input file (BED/GFF/VCF) to be used.\n"
+    info: null
+    example:
+    - "input.bed"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--input_bam"
+    alternatives:
+    - "-ibam"
+    description: "The input file is in BAM format.\nNote: BAM _must_ be sorted by\
+      \ positions.\n'--genome' option is ignored if you use '--input_bam' option!\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--genome"
+    alternatives:
+    - "-g"
+    description: "The genome file to be used.\n"
+    info: null
+    example:
+    - "genome.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    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: "--depth"
+    alternatives:
+    - "-d"
+    description: "Report the depth at each genome position (with one-based coordinates).\n\
+      Default behavior is to report a histogram.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--depth_zero"
+    alternatives:
+    - "-dz"
+    description: "Report the depth at each genome position (with zero-based coordinates).\n\
+      Reports only non-zero positions.\nDefault behavior is to report a histogram.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--bed_graph"
+    alternatives:
+    - "-bg"
+    description: "Report depth in BedGraph format. For details, see:\ngenome.ucsc.edu/goldenPath/help/bedgraph.html\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--bed_graph_zero_coverage"
+    alternatives:
+    - "-bga"
+    description: "Report depth in BedGraph format, as above (-bg).\nHowever with this\
+      \ option, regions with zero \ncoverage are also reported. This allows one to\n\
+      quickly extract all regions of a genome with 0 \ncoverage by applying: \"grep\
+      \ -w 0$\" to the output.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--split"
+    description: "Treat \"split\" BAM or BED12 entries as distinct BED intervals.\n\
+      when computing coverage.\nFor BAM files, this uses the CIGAR \"N\" and \"D\"\
+      \ operations \nto infer the blocks for computing coverage.\nFor BED12 files,\
+      \ this uses the BlockCount, BlockStarts, and BlockEnds\nfields (i.e., columns\
+      \ 10,11,12).\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--ignore_deletion"
+    alternatives:
+    - "-ignoreD"
+    description: "Ignore local deletions (CIGAR \"D\" operations) in BAM entries\n\
+      when computing coverage.\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--strand"
+    description: "Calculate coverage of intervals from a specific strand.\nWith BED\
+      \ files, requires at least 6 columns (strand is column 6). \n"
+    info: null
+    required: false
+    choices:
+    - "+"
+    - "-"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--pair_end_coverage"
+    alternatives:
+    - "-pc"
+    description: "Calculate coverage of pair-end fragments.\nWorks for BAM files only\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--fragment_size"
+    alternatives:
+    - "-fs"
+    description: "Force to use provided fragment size instead of read length\nWorks\
+      \ for BAM files only\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--du"
+    description: "Change strand af the mate read (so both reads from the same strand)\
+      \ useful for strand specific\nWorks for BAM files only\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--five_prime"
+    alternatives:
+    - "-5"
+    description: "Calculate coverage of 5\" positions (instead of entire interval).\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--three_prime"
+    alternatives:
+    - "-3"
+    description: "Calculate coverage of 3\" positions (instead of entire interval).\n"
+    info: null
+    direction: "input"
+  - type: "integer"
+    name: "--max"
+    description: "Combine all positions with a depth >= max into\na single bin in\
+      \ the histogram. Irrelevant\nfor -d and -bedGraph\n- (INTEGER)\n"
+    info: null
+    required: false
+    min: 0
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "double"
+    name: "--scale"
+    description: "Scale the coverage by a constant factor.\nEach coverage value is\
+      \ multiplied by this factor before being reported.\nUseful for normalizing coverage\
+      \ by, e.g., reads per million (RPM).\n- Default is 1.0; i.e., unscaled.\n- (FLOAT)\n"
+    info: null
+    required: false
+    min: 0.0
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--trackline"
+    description: "Adds a UCSC/Genome-Browser track line definition in the first line\
+      \ of the output.\n- See here for more details about track line definition:\n\
+      \      http://genome.ucsc.edu/goldenPath/help/bedgraph.html\n- NOTE: When adding\
+      \ a trackline definition, the output BedGraph can be easily\n      uploaded\
+      \ to the Genome Browser as a custom track,\n      BUT CAN NOT be converted into\
+      \ a BigWig file (w/o removing the first line).\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--trackopts"
+    description: "Writes additional track line definition parameters in the first\
+      \ line.\n- Example:\n  -trackopts 'name=\"My Track\" visibility=2 color=255,30,30'\n\
+      \  Note the use of single-quotes if you have spaces in your parameters.\n- (TEXT)\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Compute the coverage of a feature file among a genome.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test_data"
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "genome coverage"
+- "BED"
+- "GFF"
+- "VCF"
+- "BAM"
+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/genomecov.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: "bump_viash_0_9_4"
+  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_genomecov/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/bedtools/bedtools_genomecov"
+  executable: "target/executable/bedtools/bedtools_genomecov/bedtools_genomecov"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml

@@ -0,0 +1,262 @@
+name: "bedtools_getfasta"
+namespace: "bedtools"
+version: "bump_viash_0_9_4"
+authors:
+- name: "Dries Schaumont"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "dries@data-intuitive.com"
+      github: "DriesSchaumont"
+      orcid: "0000-0002-4389-0440"
+      linkedin: "dries-schaumont"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Scientist"
+argument_groups:
+- name: "Input arguments"
+  arguments:
+  - type: "file"
+    name: "--input_fasta"
+    description: "FASTA file containing sequences for each interval specified in the\
+      \ input BED file.\nThe headers in the input FASTA file must exactly match the\
+      \ chromosome column in the BED file.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--input_bed"
+    description: "BED file containing intervals to extract from the FASTA file.\n\
+      BED files containing a single region require a newline character\nat the end\
+      \ of the line, otherwise a blank output file is produced.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--rna"
+    description: "The FASTA is RNA not DNA. Reverse complementation handled accordingly.\n"
+    info: null
+    direction: "input"
+- name: "Run arguments"
+  arguments:
+  - type: "boolean_true"
+    name: "--strandedness"
+    alternatives:
+    - "-s"
+    description: "Force strandedness. If the feature occupies the antisense strand,\
+      \ the output sequence will\nbe reverse complemented. By default strandedness\
+      \ is not taken into account.\n"
+    info: null
+    direction: "input"
+- name: "Output arguments"
+  arguments:
+  - type: "file"
+    name: "--output"
+    alternatives:
+    - "-o"
+    description: "Output file where the output from the 'bedtools getfasta' commend\
+      \ will\nbe written to.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--tab"
+    description: "Report extract sequences in a tab-delimited format instead of in\
+      \ FASTA format.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--bed_out"
+    description: "Report extract sequences in a tab-delimited BED format instead of\
+      \ in FASTA format.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--name"
+    description: "Set the FASTA header for each extracted sequence to be the \"name\"\
+      \ and coordinate columns from the BED feature.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--name_only"
+    description: "Set the FASTA header for each extracted sequence to be the \"name\"\
+      \ columns from the BED feature.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--split"
+    description: "When --input is in BED12 format, create a separate fasta entry for\
+      \ each block in a BED12 record,\nblocks being described in the 11th and 12th\
+      \ column of the BED.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--full_header"
+    description: "Use full fasta header. By default, only the word before the first\
+      \ space or tab is used.\n"
+    info: null
+    direction: "input"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Extract sequences from a FASTA file for each of the intervals defined\
+  \ in a BED/GFF/VCF file."
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "sequencing"
+- "fasta"
+- "BED"
+- "GFF"
+- "VCF"
+license: "GPL-2.0"
+references:
+  doi:
+  - "10.1093/bioinformatics/btq033"
+links:
+  repository: "https://github.com/arq5x/bedtools2"
+  documentation: "https://bedtools.readthedocs.io/en/latest/content/tools/getfasta.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: "bump_viash_0_9_4"
+  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_getfasta/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/bedtools/bedtools_getfasta"
+  executable: "target/executable/bedtools/bedtools_getfasta/bedtools_getfasta"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/bedtools/bedtools_groupby/.config.vsh.yaml

@@ -0,0 +1,303 @@
+name: "bedtools_groupby"
+namespace: "bedtools"
+version: "bump_viash_0_9_4"
+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: "The input BED file to be used.\n"
+    info: null
+    example:
+    - "input_a.bed"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    description: "The output groupby 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: "string"
+    name: "--groupby"
+    alternatives:
+    - "-g"
+    - "-grp"
+    description: "Specify the columns (1-based) for the grouping.\nThe columns must\
+      \ be comma separated.\n- Default: 1,2,3  \n"
+    info: null
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--column"
+    alternatives:
+    - "-c"
+    - "-opCols"
+    description: "Specify the column (1-based) that should be summarized.\n"
+    info: null
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--operation"
+    alternatives:
+    - "-o"
+    - "-ops"
+    description: "Specify the operation that should be applied to opCol.\nValid operations:\n\
+      \    sum, count, count_distinct, min, max,\n    mean, median, mode, antimode,\n\
+      \    stdev, sstdev (sample standard dev.),\n    collapse (i.e., print a comma\
+      \ separated list (duplicates allowed)), \n    distinct (i.e., print a comma\
+      \ separated list (NO duplicates allowed)), \n    distinct_sort_num (as distinct,\
+      \ but sorted numerically, ascending), \n    distinct_sort_num_desc (as distinct,\
+      \ but sorted numerically, descending), \n    concat   (i.e., merge values into\
+      \ a single, non-delimited string), \n    freqdesc (i.e., print desc. list of\
+      \ values:freq)\n    freqasc (i.e., print asc. list of values:freq)\n    first\
+      \ (i.e., print first value)\n    last (i.e., print last value)\n\nDefault value:\
+      \ sum   \n\nIf there is only column, but multiple operations, all operations\
+      \ will be\napplied on that column. Likewise, if there is only one operation,\
+      \ but\nmultiple columns, that operation will be applied to all columns.\nOtherwise,\
+      \ the number of columns must match the the number of operations,\nand will be\
+      \ applied in respective order.\nE.g., \"-c 5,4,6 -o sum,mean,count\" will give\
+      \ the sum of column 5,\nthe mean of column 4, and the count of column 6.\nThe\
+      \ order of output columns will match the ordering given in the command.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--full"
+    description: "Print all columns from input file. The first line in the group is\
+      \ used.\nDefault: print only grouped columns.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--inheader"
+    description: "Input file has a header line - the first line will be ignored.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--outheader"
+    description: "Print header line in the output, detailing the column names. \n\
+      If the input file has headers (-inheader), the output file\nwill use the input's\
+      \ column names.\nIf the input file has no headers, the output file\nwill use\
+      \ \"col_1\", \"col_2\", etc. as the column names.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--header"
+    description: "same as '-inheader -outheader'."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--ignorecase"
+    description: "Group values regardless of upper/lower case.\n"
+    info: null
+    direction: "input"
+  - type: "integer"
+    name: "--precision"
+    alternatives:
+    - "-prec"
+    description: "Sets the decimal precision for output. \n"
+    info: null
+    default:
+    - 5
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--delimiter"
+    alternatives:
+    - "-delim"
+    description: "Specify a custom delimiter for the collapse operations.\n"
+    info: null
+    example:
+    - "|"
+    default:
+    - ","
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Summarizes a dataset column based upon common column groupings. \nAkin\
+  \ to the SQL \"group by\" command.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "groupby"
+- "BED"
+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/groupby.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: "bump_viash_0_9_4"
+  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_groupby/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/bedtools/bedtools_groupby"
+  executable: "target/executable/bedtools/bedtools_groupby/bedtools_groupby"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/bedtools/bedtools_intersect/.config.vsh.yaml

@@ -0,0 +1,440 @@
+name: "bedtools_intersect"
+namespace: "bedtools"
+version: "bump_viash_0_9_4"
+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"
+scope:
+  image: "public"
+  target: "public"
+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: "bump_viash_0_9_4"
+  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: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/bedtools/bedtools_links/.config.vsh.yaml

@@ -0,0 +1,240 @@
+name: "bedtools_links"
+namespace: "bedtools"
+version: "bump_viash_0_9_4"
+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 file (bed/gff/vcf)."
+    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 HTML file to be written."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Options"
+  description: "By default, the links created will point to human (hg18) UCSC browser.\n\
+    If you have a local mirror, you can override this behavior by supplying\nthe -base,\
+    \ -org, and -db options.\n\nFor example, if the URL of your local mirror for mouse\
+    \ MM9 is called: \nhttp://mymirror.myuniversity.edu, then you would use the following:\n\
+    --base_url http://mymirror.myuniversity.edu\n--organism mouse\n--database mm9\n"
+  arguments:
+  - type: "string"
+    name: "--base_url"
+    alternatives:
+    - "-base"
+    description: "The “basename” for the UCSC browser.\n"
+    info: null
+    default:
+    - "http://genome.ucsc.edu"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--organism"
+    alternatives:
+    - "-org"
+    description: "The organism (e.g. mouse, human). \n"
+    info: null
+    default:
+    - "human"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--database"
+    alternatives:
+    - "-db"
+    description: "The genome build. \n"
+    info: null
+    default:
+    - "hg18"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Creates an HTML file with links to an instance of the UCSC Genome Browser\
+  \ for all features / intervals in a file. \nThis is useful for cases when one wants\
+  \ to manually inspect through a large set of annotations or features.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "Links"
+- "BED"
+- "GFF"
+- "VCF"
+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/links.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: "bump_viash_0_9_4"
+  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_links/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/bedtools/bedtools_links"
+  executable: "target/executable/bedtools/bedtools_links/bedtools_links"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/bedtools/bedtools_merge/.config.vsh.yaml

@@ -0,0 +1,309 @@
+name: "bedtools_merge"
+namespace: "bedtools"
+version: "bump_viash_0_9_4"
+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 file (BED/GFF/VCF) to be merged."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    description: "Output merged file BED to be written."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Options"
+  arguments:
+  - type: "boolean_true"
+    name: "--strand"
+    alternatives:
+    - "-s"
+    description: "Force strandedness. That is, only merge features\nthat are on the\
+      \ same strand.\n- By default, merging is done without respect to strand.\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--specific_strand"
+    alternatives:
+    - "-S"
+    description: "Force merge for one specific strand only.\nFollow with + or - to\
+      \ force merge from only\nthe forward or reverse strand, respectively.\n- By\
+      \ default, merging is done without respect to strand.\n"
+    info: null
+    required: false
+    choices:
+    - "+"
+    - "-"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--distance"
+    alternatives:
+    - "-d"
+    description: "Maximum distance between features allowed for features\nto be merged.\n\
+      - Def. 0. That is, overlapping & book-ended features are merged.\n- (INTEGER)\n\
+      - Note: negative values enforce the number of b.p. required for overlap.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--columns"
+    alternatives:
+    - "-c"
+    description: "Specify columns from the B file to map onto intervals in A.\nDefault:\
+      \ 5.\nMultiple columns can be specified in a comma-delimited list.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--operation"
+    alternatives:
+    - "-o"
+    description: "Specify the operation that should be applied to -c.\nValid operations:\n\
+      \    sum, min, max, absmin, absmax,\n    mean, median, mode, antimode\n    stdev,\
+      \ sstdev\n    collapse (i.e., print a delimited list (duplicates allowed)),\
+      \ \n    distinct (i.e., print a delimited list (NO duplicates allowed)), \n\
+      \    distinct_sort_num (as distinct, sorted numerically, ascending),\n    distinct_sort_num_desc\
+      \ (as distinct, sorted numerically, desscending),\n    distinct_only (delimited\
+      \ list of only unique values),\n    count\n    count_distinct (i.e., a count\
+      \ of the unique values in the column), \n    first (i.e., just the first value\
+      \ in the column), \n    last (i.e., just the last value in the column), \nDefault:\
+      \ sum\nMultiple operations can be specified in a comma-delimited list.\n\nIf\
+      \ there is only column, but multiple operations, all operations will be\napplied\
+      \ on that column. Likewise, if there is only one operation, but\nmultiple columns,\
+      \ that operation will be applied to all columns.\nOtherwise, the number of columns\
+      \ must match the the number of operations,\nand will be applied in respective\
+      \ order.\nE.g., \"-c 5,4,6 -o sum,mean,count\" will give the sum of column 5,\n\
+      the mean of column 4, and the count of column 6.\nThe order of output columns\
+      \ will match the ordering given in the command.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--delimiter"
+    alternatives:
+    - "-delim"
+    description: "Specify a custom delimiter for the collapse operations.\n"
+    info: null
+    example:
+    - "|"
+    default:
+    - ","
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--precision"
+    alternatives:
+    - "-prec"
+    description: "Sets the decimal precision for output (Default: 5).\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--bed"
+    description: "If using BAM input, write output as BED.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--header"
+    description: "Print the header from the A file prior to results.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_buffer"
+    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"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Merges overlapping BED/GFF/VCF entries into a single interval.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test_data"
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+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/merge.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: "bump_viash_0_9_4"
+  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_merge/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/bedtools/bedtools_merge"
+  executable: "target/executable/bedtools/bedtools_merge/bedtools_merge"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/bedtools/bedtools_sort/.config.vsh.yaml

@@ -0,0 +1,252 @@
+name: "bedtools_sort"
+namespace: "bedtools"
+version: "bump_viash_0_9_4"
+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 file (bed/gff/vcf) to be sorted."
+    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 sorted file (bed/gff/vcf) to be written."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Options"
+  arguments:
+  - type: "boolean_true"
+    name: "--sizeA"
+    description: "Sort by feature size in ascending order."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--sizeD"
+    description: "Sort by feature size in descending order."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--chrThenSizeA"
+    description: "Sort by chrom (asc), then feature size (asc)."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--chrThenSizeD"
+    description: "Sort by chrom (asc), then feature size (desc)."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--chrThenScoreA"
+    description: "Sort by chrom (asc), then score (asc)."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--chrThenScoreD"
+    description: "Sort by chrom (asc), then score (desc)."
+    info: null
+    direction: "input"
+  - type: "file"
+    name: "--genome"
+    alternatives:
+    - "-g"
+    description: "Sort according to the chromosomes declared in \"genome.txt\""
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--faidx"
+    description: "Sort according to the chromosomes declared in \"names.txt\""
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--header"
+    description: "Print the header from the A file prior to results."
+    info: null
+    direction: "input"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Sorts a feature file (bed/gff/vcf) by chromosome and other criteria."
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "sort"
+- "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/sort.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: "bump_viash_0_9_4"
+  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_sort/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/bedtools/bedtools_sort"
+  executable: "target/executable/bedtools/bedtools_sort/bedtools_sort"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

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

@@ -0,0 +1,188 @@
+name: "busco_download_datasets"
+namespace: "busco"
+version: "bump_viash_0_9_4"
+authors:
+- name: "Dorien Roosen"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "dorien@data-intuitive.com"
+      github: "dorien-er"
+      linkedin: "dorien-roosen"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Scientist"
+argument_groups:
+- name: "Inputs"
+  arguments:
+  - type: "string"
+    name: "--download"
+    description: "Download dataset. Possible values are a specific dataset name, \"\
+      all\", \"prokaryota\", \"eukaryota\", or \"virus\".\nThe full list of available\
+      \ datasets can be viewed [here](https://busco-data.ezlab.org/v5/data/lineages/)\
+      \ or by running the busco/busco_list_datasets component.\n"
+    info: null
+    example:
+    - "stramenopiles_odb10"
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--download_path"
+    description: "Local filepath for storing BUSCO dataset downloads\n"
+    info: null
+    example:
+    - "busco_downloads"
+    default:
+    - "busco_downloads"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Downloads available busco datasets"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "lineage datasets"
+license: "MIT"
+references:
+  doi:
+  - "10.1007/978-1-4939-9173-0_14"
+links:
+  repository: "https://gitlab.com/ezlab/busco"
+  homepage: "https://busco.ezlab.org/"
+  documentation: "https://busco.ezlab.org/busco_userguide.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: "quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0"
+  target_registry: "images.viash-hub.com"
+  target_tag: "bump_viash_0_9_4"
+  namespace_separator: "/"
+  setup:
+  - type: "docker"
+    run:
+    - "busco --version | sed 's/BUSCO\\s\\(.*\\)/busco: \"\\1\"/' > /var/software_versions.txt\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/busco/busco_download_datasets/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/busco/busco_download_datasets"
+  executable: "target/executable/busco/busco_download_datasets/busco_download_datasets"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

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

@@ -0,0 +1,175 @@
+name: "busco_list_datasets"
+namespace: "busco"
+version: "bump_viash_0_9_4"
+authors:
+- name: "Dorien Roosen"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "dorien@data-intuitive.com"
+      github: "dorien-er"
+      linkedin: "dorien-roosen"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Scientist"
+argument_groups:
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    alternatives:
+    - "-o"
+    description: "Output file of the available busco datasets\n"
+    info: null
+    example:
+    - "file.txt"
+    default:
+    - "busco_dataset_list.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Lists the available busco datasets"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "lineage datasets"
+license: "MIT"
+references:
+  doi:
+  - "10.1007/978-1-4939-9173-0_14"
+links:
+  repository: "https://gitlab.com/ezlab/busco"
+  homepage: "https://busco.ezlab.org/"
+  documentation: "https://busco.ezlab.org/busco_userguide.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: "quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0"
+  target_registry: "images.viash-hub.com"
+  target_tag: "bump_viash_0_9_4"
+  namespace_separator: "/"
+  setup:
+  - type: "docker"
+    run:
+    - "busco --version | sed 's/BUSCO\\s\\(.*\\)/busco: \"\\1\"/' > /var/software_versions.txt\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/busco/busco_list_datasets/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/busco/busco_list_datasets"
+  executable: "target/executable/busco/busco_list_datasets/busco_list_datasets"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

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

@@ -0,0 +1,453 @@
+name: "busco_run"
+namespace: "busco"
+version: "bump_viash_0_9_4"
+authors:
+- name: "Dorien Roosen"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "dorien@data-intuitive.com"
+      github: "dorien-er"
+      linkedin: "dorien-roosen"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Scientist"
+argument_groups:
+- name: "Inputs"
+  arguments:
+  - type: "file"
+    name: "--input"
+    alternatives:
+    - "-i"
+    description: "Input sequence file in FASTA format. Can be an assembled genome\
+      \ or transcriptome (DNA), or protein sequences from an annotated gene set. Also\
+      \ possible to use a path to a directory containing multiple input files.\n"
+    info: null
+    example:
+    - "file.fasta"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--mode"
+    alternatives:
+    - "-m"
+    description: "Specify which BUSCO analysis mode to run. There are three valid\
+      \ modes:\n  - geno or genome, for genome assemblies (DNA)\n  - tran or transcriptome,\
+      \ for transcriptome assemblies (DNA)\n  - prot or proteins, for annotated gene\
+      \ sets (protein)\n"
+    info: null
+    example:
+    - "proteins"
+    required: true
+    choices:
+    - "genome"
+    - "geno"
+    - "transcriptome"
+    - "tran"
+    - "proteins"
+    - "prot"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--lineage_dataset"
+    alternatives:
+    - "-l"
+    description: "Specify a BUSCO lineage dataset that is most closely related to\
+      \ the assembly or gene set being assessed. \nThe full list of available datasets\
+      \ can be viewed [here](https://busco-data.ezlab.org/v5/data/lineages/) or by\
+      \ running the busco/busco_list_datasets component.\nWhen unsure, the \"--auto_lineage\"\
+      \ flag can be set to automatically find the optimal lineage path.\nBUSCO will\
+      \ automatically download the requested dataset if it is not already present\
+      \ in the download folder. \nYou can optionally provide a path to a local dataset\
+      \ instead of a name, e.g. path/to/dataset.\nDatasets can be downloaded using\
+      \ the busco/busco_download_dataset component.\n"
+    info: null
+    example:
+    - "stramenopiles_odb10"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--short_summary_json"
+    description: "Output file for short summary in JSON format.\n"
+    info: null
+    example:
+    - "short_summary.json"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--short_summary_txt"
+    description: "Output file for short summary in TXT format.\n"
+    info: null
+    example:
+    - "short_summary.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--full_table"
+    description: "Full table output in TSV format.\n"
+    info: null
+    example:
+    - "full_table.tsv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--missing_busco_list"
+    description: "Missing list output in TSV format.\n"
+    info: null
+    example:
+    - "missing_busco_list.tsv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_dir"
+    description: "The full output directory, if so desired.\n"
+    info: null
+    example:
+    - "output_dir"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Resource and Run Settings"
+  arguments:
+  - type: "boolean_true"
+    name: "--force"
+    description: "Force rewriting of existing files. Must be used when output files\
+      \ with the provided name already exist.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--quiet"
+    alternatives:
+    - "-q"
+    description: "Disable the info logs, displays only errors.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--restart"
+    alternatives:
+    - "-r"
+    description: "Continue a run that had already partially completed. Restarting\
+      \ skips calls to tools that have completed but performs all pre- and post-processing\
+      \ steps.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--tar"
+    description: "Compress some subdirectories with many files to save space.\n"
+    info: null
+    direction: "input"
+- name: "Lineage Dataset Settings"
+  arguments:
+  - type: "boolean_true"
+    name: "--auto_lineage"
+    description: "Run auto-lineage pipelilne to automatically determine BUSCO lineage\
+      \ dataset that is most closely related to the assembly or gene set being assessed.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--auto_lineage_euk"
+    description: "Run auto-placement just on eukaryota tree to find optimal lineage\
+      \ path.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--auto_lineage_prok"
+    description: "Run auto_lineage just on prokaryota trees to find optimum lineage\
+      \ path.\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--datasets_version"
+    description: "Specify the version of BUSCO datasets\n"
+    info: null
+    example:
+    - "odb10"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Augustus Settings"
+  arguments:
+  - type: "boolean_true"
+    name: "--augustus"
+    description: "Use augustus gene predictor for eukaryote runs.\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--augustus_parameters"
+    description: "Additional parameters to be passed to Augustus (see Augustus documentation:\
+      \ https://github.com/Gaius-Augustus/Augustus/blob/master/docs/RUNNING-AUGUSTUS.md).\n\
+      Parameters should be contained within a single string, without whitespace and\
+      \ seperated by commas.\n"
+    info: null
+    example:
+    - "--PARAM1=VALUE1,--PARAM2=VALUE2"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--augustus_species"
+    description: "Specify the augustus species\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--long"
+    description: "Optimize Augustus self-training mode. This adds considerably to\
+      \ the run time, but can improve results for some non-model organisms.\n"
+    info: null
+    direction: "input"
+- name: "BBTools Settings"
+  arguments:
+  - type: "integer"
+    name: "--contig_break"
+    description: "Number of contiguous Ns to signify a break between contigs in BBTools\
+      \ analysis.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--limit"
+    description: "Number of candidate regions (contig or transcript) from the BLAST\
+      \ output to consider per BUSCO.\nThis option is only effective in pipelines\
+      \ using BLAST, i.e. the genome pipeline (see --augustus) or the prokaryota transcriptome\
+      \ pipeline.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--scaffold_composition"
+    description: "Writes ACGTN content per scaffold to a file scaffold_composition.txt.\n"
+    info: null
+    direction: "input"
+- name: "BLAST Settings"
+  arguments:
+  - type: "double"
+    name: "--e_value"
+    description: "E-value cutoff for BLAST searches.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Protein Gene Prediction settings"
+  arguments:
+  - type: "boolean_true"
+    name: "--miniprot"
+    description: "Use Miniprot gene predictor.\n"
+    info: null
+    direction: "input"
+- name: "MetaEuk Settings"
+  arguments:
+  - type: "boolean_true"
+    name: "--metaeuk"
+    description: "Use Metaeuk gene predictor.\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--metaeuk_parameters"
+    description: "Pass additional arguments to Metaeuk for the first run (see Metaeuk\
+      \ documentation https://github.com/soedinglab/metaeuk).\nAll parameters should\
+      \ be contained within a single string with no white space, with each parameter\
+      \ separated by a comma.\n"
+    info: null
+    example:
+    - "--max-overlap=15,--min-exon-aa=15"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--metaeuk_rerun_parameters"
+    description: "Pass additional arguments to Metaeuk for the second run (see Metaeuk\
+      \ documentation https://github.com/soedinglab/metaeuk).\nAll parameters should\
+      \ be contained within a single string with no white space, with each parameter\
+      \ separated by a comma.\n"
+    info: null
+    example:
+    - "--max-overlap=15,--min-exon-aa=15"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Assessment of genome assembly and annotation completeness with single\
+  \ copy orthologs"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test_data"
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "Genome assembly"
+- "quality control"
+license: "MIT"
+references:
+  doi:
+  - "10.1007/978-1-4939-9173-0_14"
+links:
+  repository: "https://gitlab.com/ezlab/busco"
+  homepage: "https://busco.ezlab.org/"
+  documentation: "https://busco.ezlab.org/busco_userguide.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: "quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0"
+  target_registry: "images.viash-hub.com"
+  target_tag: "bump_viash_0_9_4"
+  namespace_separator: "/"
+  setup:
+  - type: "docker"
+    run:
+    - "busco --version | sed 's/BUSCO\\s\\(.*\\)/busco: \"\\1\"/' > /var/software_versions.txt\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/busco/busco_run/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/busco/busco_run"
+  executable: "target/executable/busco/busco_run/busco_run"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/cellranger/cellranger_mkref/.config.vsh.yaml

@@ -0,0 +1,225 @@
+name: "cellranger_mkref"
+namespace: "cellranger"
+version: "bump_viash_0_9_4"
+authors:
+- name: "Emma Rousseau"
+  roles:
+  - "author"
+  info:
+    links:
+      email: "emma@data-intuitive.com"
+      github: "emmarousseau"
+      linkedin: "emmarousseau1"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Bioinformatician"
+argument_groups:
+- name: "Arguments"
+  arguments:
+  - type: "file"
+    name: "--genome_fasta"
+    description: "Reference genome fasta."
+    info: null
+    example:
+    - "genome_sequence.fa.gz"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--transcriptome_gtf"
+    description: "Reference transcriptome annotation."
+    info: null
+    example:
+    - "transcriptome_annotation.gtf.gz"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--reference_version"
+    description: "Optional reference version string to include with reference"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output"
+    description: "Output folder"
+    info: null
+    example:
+    - "cellranger_reference"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Build a Cell Ranger-compatible reference folder from user-supplied genome\
+  \ FASTA and gene GTF files."
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test_data"
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "cellranger"
+- "single-cell"
+- "rna-seq"
+- "alignment"
+- "reference"
+- "gtf"
+- "fasta"
+license: "Proprietary"
+references:
+  doi:
+  - "10.1038/ncomms14049"
+links:
+  repository: "https://github.com/10XGenomics/cellranger/blob/main/lib/python/cellranger/reference_builder.py"
+  homepage: "https://www.10xgenomics.com/support/software/cell-ranger/latest"
+  documentation: "https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references"
+  issue_tracker: "https://github.com/10XGenomics/cellranger/issues"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    label:
+    - "highmem"
+    - "highcpu"
+    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: "ghcr.io/data-intuitive/cellranger:8.0"
+  target_registry: "images.viash-hub.com"
+  target_tag: "bump_viash_0_9_4"
+  namespace_separator: "/"
+  setup:
+  - type: "apt"
+    packages:
+    - "procps"
+    - "pigz"
+    interactive: false
+  test_setup:
+  - type: "apt"
+    packages:
+    - "seqkit"
+    interactive: false
+  - type: "docker"
+    run:
+    - "cellranger --version | sed 's/ cellranger-/: /' > /var/software_versions.txt\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/cellranger/cellranger_mkref/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/cellranger/cellranger_mkref"
+  executable: "target/executable/cellranger/cellranger_mkref/cellranger_mkref"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/cutadapt/.config.vsh.yaml

@@ -0,0 +1,770 @@
+name: "cutadapt"
+version: "bump_viash_0_9_4"
+authors:
+- name: "Toni Verbeiren"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      github: "tverbeiren"
+      linkedin: "verbeiren"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Scientist and CEO"
+argument_groups:
+- name: "Specify Adapters for R1"
+  arguments:
+  - type: "string"
+    name: "--adapter"
+    alternatives:
+    - "-a"
+    description: "Sequence of an adapter ligated to the 3' end (paired data:\nof the\
+      \ first read). The adapter and subsequent bases are\ntrimmed. If a '$' character\
+      \ is appended ('anchoring'), the\nadapter is only found if it is a suffix of\
+      \ the read.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+  - type: "string"
+    name: "--front"
+    alternatives:
+    - "-g"
+    description: "Sequence of an adapter ligated to the 5' end (paired data:\nof the\
+      \ first read). The adapter and any preceding bases\nare trimmed. Partial matches\
+      \ at the 5' end are allowed. If\na '^' character is prepended ('anchoring'),\
+      \ the adapter is\nonly found if it is a prefix of the read.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+  - type: "string"
+    name: "--anywhere"
+    alternatives:
+    - "-b"
+    description: "Sequence of an adapter that may be ligated to the 5' or 3'\nend\
+      \ (paired data: of the first read). Both types of\nmatches as described under\
+      \ -a and -g are allowed. If the\nfirst base of the read is part of the match,\
+      \ the behavior\nis as with -g, otherwise as with -a. This option is mostly\n\
+      for rescuing failed library preparations - do not use if\nyou know which end\
+      \ your adapter was ligated to!\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+- name: "Specify Adapters using Fasta files for R1"
+  arguments:
+  - type: "file"
+    name: "--adapter_fasta"
+    description: "Fasta file containing sequences of an adapter ligated to the 3'\
+      \ end (paired data:\nof the first read). The adapter and subsequent bases are\n\
+      trimmed. If a '$' character is appended ('anchoring'), the\nadapter is only\
+      \ found if it is a suffix of the read.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+  - type: "file"
+    name: "--front_fasta"
+    description: "Fasta file containing sequences of an adapter ligated to the 5'\
+      \ end (paired data:\nof the first read). The adapter and any preceding bases\n\
+      are trimmed. Partial matches at the 5' end are allowed. If\na '^' character\
+      \ is prepended ('anchoring'), the adapter is\nonly found if it is a prefix of\
+      \ the read.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--anywhere_fasta"
+    description: "Fasta file containing sequences of an adapter that may be ligated\
+      \ to the 5' or 3'\nend (paired data: of the first read). Both types of\nmatches\
+      \ as described under -a and -g are allowed. If the\nfirst base of the read is\
+      \ part of the match, the behavior\nis as with -g, otherwise as with -a. This\
+      \ option is mostly\nfor rescuing failed library preparations - do not use if\n\
+      you know which end your adapter was ligated to!\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Specify Adapters for R2"
+  arguments:
+  - type: "string"
+    name: "--adapter_r2"
+    alternatives:
+    - "-A"
+    description: "Sequence of an adapter ligated to the 3' end (paired data:\nof the\
+      \ first read). The adapter and subsequent bases are\ntrimmed. If a '$' character\
+      \ is appended ('anchoring'), the\nadapter is only found if it is a suffix of\
+      \ the read.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+  - type: "string"
+    name: "--front_r2"
+    alternatives:
+    - "-G"
+    description: "Sequence of an adapter ligated to the 5' end (paired data:\nof the\
+      \ first read). The adapter and any preceding bases\nare trimmed. Partial matches\
+      \ at the 5' end are allowed. If\na '^' character is prepended ('anchoring'),\
+      \ the adapter is\nonly found if it is a prefix of the read.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+  - type: "string"
+    name: "--anywhere_r2"
+    alternatives:
+    - "-B"
+    description: "Sequence of an adapter that may be ligated to the 5' or 3'\nend\
+      \ (paired data: of the first read). Both types of\nmatches as described under\
+      \ -a and -g are allowed. If the\nfirst base of the read is part of the match,\
+      \ the behavior\nis as with -g, otherwise as with -a. This option is mostly\n\
+      for rescuing failed library preparations - do not use if\nyou know which end\
+      \ your adapter was ligated to!\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+- name: "Specify Adapters using Fasta files for R2"
+  arguments:
+  - type: "file"
+    name: "--adapter_r2_fasta"
+    description: "Fasta file containing sequences of an adapter ligated to the 3'\
+      \ end (paired data:\nof the first read). The adapter and subsequent bases are\n\
+      trimmed. If a '$' character is appended ('anchoring'), the\nadapter is only\
+      \ found if it is a suffix of the read.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--front_r2_fasta"
+    description: "Fasta file containing sequences of an adapter ligated to the 5'\
+      \ end (paired data:\nof the first read). The adapter and any preceding bases\n\
+      are trimmed. Partial matches at the 5' end are allowed. If\na '^' character\
+      \ is prepended ('anchoring'), the adapter is\nonly found if it is a prefix of\
+      \ the read.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--anywhere_r2_fasta"
+    description: "Fasta file containing sequences of an adapter that may be ligated\
+      \ to the 5' or 3'\nend (paired data: of the first read). Both types of\nmatches\
+      \ as described under -a and -g are allowed. If the\nfirst base of the read is\
+      \ part of the match, the behavior\nis as with -g, otherwise as with -a. This\
+      \ option is mostly\nfor rescuing failed library preparations - do not use if\n\
+      you know which end your adapter was ligated to!\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Paired-end options"
+  arguments:
+  - type: "boolean_true"
+    name: "--pair_adapters"
+    description: "Treat adapters given with -a/-A etc. as pairs. Either both\nor none\
+      \ are removed from each read pair.\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--pair_filter"
+    description: "Which of the reads in a paired-end read have to match the\nfiltering\
+      \ criterion in order for the pair to be filtered.\n"
+    info: null
+    required: false
+    choices:
+    - "any"
+    - "both"
+    - "first"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--interleaved"
+    description: "Read and/or write interleaved paired-end reads.\n"
+    info: null
+    direction: "input"
+- name: "Input parameters"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "Input fastq file for single-end reads or R1 for paired-end reads.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--input_r2"
+    description: "Input fastq file for R2 in the case of paired-end reads.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "double"
+    name: "--error_rate"
+    alternatives:
+    - "-E"
+    - "--errors"
+    description: "Maximum allowed error rate (if 0 <= E < 1), or absolute\nnumber\
+      \ of errors for full-length adapter match (if E is an\ninteger >= 1). Error\
+      \ rate = no. of errors divided by\nlength of matching region. Default: 0.1 (10%).\n"
+    info: null
+    example:
+    - 0.1
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--no_indels"
+    description: "Allow only mismatches in alignments.\n"
+    info: null
+    direction: "input"
+  - type: "integer"
+    name: "--times"
+    alternatives:
+    - "-n"
+    description: "Remove up to COUNT adapters from each read. Default: 1.\n"
+    info: null
+    example:
+    - 1
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--overlap"
+    alternatives:
+    - "-O"
+    description: "Require MINLENGTH overlap between read and adapter for an\nadapter\
+      \ to be found. The default is 3.\n"
+    info: null
+    example:
+    - 3
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--match_read_wildcards"
+    description: "Interpret IUPAC wildcards in reads.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_match_adapter_wildcards"
+    description: "Do not interpret IUPAC wildcards in adapters.\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--action"
+    description: "What to do if a match was found. trim: trim adapter and\nup- or\
+      \ downstream sequence; retain: trim, but retain\nadapter; mask: replace with\
+      \ 'N' characters; lowercase:\nconvert to lowercase; none: leave unchanged.\n\
+      The default is trim.\n"
+    info: null
+    example:
+    - "trim"
+    required: false
+    choices:
+    - "trim"
+    - "retain"
+    - "mask"
+    - "lowercase"
+    - "none"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--revcomp"
+    alternatives:
+    - "--rc"
+    description: "Check both the read and its reverse complement for adapter\nmatches.\
+      \ If match is on reverse-complemented version,\noutput that one.\n"
+    info: null
+    direction: "input"
+- name: "Demultiplexing options"
+  arguments:
+  - type: "string"
+    name: "--demultiplex_mode"
+    description: "Enable demultiplexing and set the mode for it.\nWith mode 'unique_dual',\
+      \ adapters from the first and second read are used,\nand the indexes from the\
+      \ reads are only used in pairs. This implies\n--pair_adapters.\nEnabling mode\
+      \ 'combinatorial_dual' allows all combinations of the sets of indexes\non R1\
+      \ and R2. It is necessary to write each read pair to an output\nfile depending\
+      \ on the adapters found on both R1 and R2.\nMode 'single', uses indexes or barcodes\
+      \ located at the 5'\nend of the R1 read (single). \n"
+    info: null
+    required: false
+    choices:
+    - "single"
+    - "unique_dual"
+    - "combinatorial_dual"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Read modifications"
+  arguments:
+  - type: "integer"
+    name: "--cut"
+    alternatives:
+    - "-u"
+    description: "Remove LEN bases from each read (or R1 if paired; use --cut_r2\n\
+      option for R2). If LEN is positive, remove bases from the\nbeginning. If LEN\
+      \ is negative, remove bases from the end.\nCan be used twice if LENs have different\
+      \ signs. Applied\n*before* adapter trimming.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--cut_r2"
+    description: "Remove LEN bases from each read (for R2). If LEN is positive, remove\
+      \ bases from the\nbeginning. If LEN is negative, remove bases from the end.\n\
+      Can be used twice if LENs have different signs. Applied\n*before* adapter trimming.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+  - type: "string"
+    name: "--nextseq_trim"
+    description: "NextSeq-specific quality trimming (each read). Trims also\ndark\
+      \ cycles appearing as high-quality G bases.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--quality_cutoff"
+    alternatives:
+    - "-q"
+    description: "Trim low-quality bases from 5' and/or 3' ends of each read\nbefore\
+      \ adapter removal. Applied to both reads if data is\npaired. If one value is\
+      \ given, only the 3' end is trimmed.\nIf two comma-separated cutoffs are given,\
+      \ the 5' end is\ntrimmed with the first cutoff, the 3' end with the second.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--quality_cutoff_r2"
+    alternatives:
+    - "-Q"
+    description: "Quality-trimming cutoff for R2. Default: same as for R1\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--quality_base"
+    description: "Assume that quality values in FASTQ are encoded as\nascii(quality\
+      \ + N). This needs to be set to 64 for some\nold Illumina FASTQ files. The default\
+      \ is 33.\n"
+    info: null
+    example:
+    - 33
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--poly_a"
+    description: "Trim poly-A tails"
+    info: null
+    direction: "input"
+  - type: "integer"
+    name: "--length"
+    alternatives:
+    - "-l"
+    description: "Shorten reads to LENGTH. Positive values remove bases at\nthe end\
+      \ while negative ones remove bases at the beginning.\nThis and the following\
+      \ modifications are applied after\nadapter trimming.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--trim_n"
+    description: "Trim N's on ends of reads."
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--length_tag"
+    description: "Search for TAG followed by a decimal number in the\ndescription\
+      \ field of the read. Replace the decimal number\nwith the correct length of\
+      \ the trimmed read. For example,\nuse --length-tag 'length=' to correct fields\
+      \ like\n'length=123'.\n"
+    info: null
+    example:
+    - "length="
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--strip_suffix"
+    description: "Remove this suffix from read names if present. Can be\ngiven multiple\
+      \ times.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--prefix"
+    alternatives:
+    - "-x"
+    description: "Add this prefix to read names. Use {name} to insert the\nname of\
+      \ the matching adapter.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--suffix"
+    alternatives:
+    - "-y"
+    description: "Add this suffix to read names; can also include {name}\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--rename"
+    description: "Rename reads using TEMPLATE containing variables such as\n{id},\
+      \ {adapter_name} etc. (see documentation)\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--zero_cap"
+    alternatives:
+    - "-z"
+    description: "Change negative quality values to zero."
+    info: null
+    direction: "input"
+- name: "Filtering of processed reads"
+  description: "Filters are applied after above read modifications. Paired-end reads\
+    \ are\nalways discarded pairwise (see also --pair_filter).\n"
+  arguments:
+  - type: "string"
+    name: "--minimum_length"
+    alternatives:
+    - "-m"
+    description: "Discard reads shorter than LEN. Default is 0.\nWhen trimming paired-end\
+      \ reads, the minimum lengths for R1 and R2 can be specified separately by separating\
+      \ them with a colon (:).\nIf the colon syntax is not used, the same minimum\
+      \ length applies to both reads, as discussed above.\nAlso, one of the values\
+      \ can be omitted to impose no restrictions.\nFor example, with -m 17:, the length\
+      \ of R1 must be at least 17, but the length of R2 is ignored.\n"
+    info: null
+    example:
+    - "0"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--maximum_length"
+    alternatives:
+    - "-M"
+    description: "Discard reads longer than LEN. Default: no limit.\nFor paired reads,\
+      \ see the remark for --minimum_length\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--max_n"
+    description: "Discard reads with more than COUNT 'N' bases. If COUNT is\na number\
+      \ between 0 and 1, it is interpreted as a fraction\nof the read length.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "long"
+    name: "--max_expected_errors"
+    alternatives:
+    - "--max_ee"
+    description: "Discard reads whose expected number of errors (computed\nfrom quality\
+      \ values) exceeds ERRORS.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "long"
+    name: "--max_average_error_rate"
+    alternatives:
+    - "--max_aer"
+    description: "as --max_expected_errors (see above), but divided by\nlength to\
+      \ account for reads of varying length.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--discard_trimmed"
+    alternatives:
+    - "--discard"
+    description: "Discard reads that contain an adapter. Use also -O to\navoid discarding\
+      \ too many randomly matching reads.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--discard_untrimmed"
+    alternatives:
+    - "--trimmed_only"
+    description: "Discard reads that do not contain an adapter.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--discard_casava"
+    description: "Discard reads that did not pass CASAVA filtering (header\nhas :Y:).\n"
+    info: null
+    direction: "input"
+- name: "Output parameters"
+  arguments:
+  - type: "string"
+    name: "--report"
+    description: "Which type of report to print: 'full' (default) or 'minimal'.\n"
+    info: null
+    example:
+    - "full"
+    required: false
+    choices:
+    - "full"
+    - "minimal"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--json"
+    description: "Write report in JSON format to this file.\n"
+    info: null
+    direction: "input"
+  - type: "file"
+    name: "--output"
+    description: "Glob pattern for matching the expected output files.\nShould include\
+      \ `$output_dir`.\n"
+    info: null
+    example:
+    - "fastq/*_001.fast[a,q]"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: true
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--fasta"
+    description: "Output FASTA to standard output even on FASTQ input.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--info_file"
+    description: "Write information about each read and its adapter matches\ninto\
+      \ info.txt in the output directory.\nSee the documentation for the file format.\n"
+    info: null
+    direction: "input"
+- name: "Debug"
+  arguments:
+  - type: "boolean_true"
+    name: "--debug"
+    description: "Print debug information"
+    info: null
+    direction: "input"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Cutadapt removes adapter sequences from high-throughput sequencing reads.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "RNA-seq"
+- "scRNA-seq"
+- "high-throughput"
+license: "MIT"
+references:
+  doi:
+  - "10.14806/ej.17.1.200"
+links:
+  repository: "https://github.com/marcelm/cutadapt"
+  homepage: "https://cutadapt.readthedocs.io"
+  documentation: "https://cutadapt.readthedocs.io"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$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: "python:3.12"
+  target_registry: "images.viash-hub.com"
+  target_tag: "bump_viash_0_9_4"
+  namespace_separator: "/"
+  setup:
+  - type: "python"
+    user: false
+    pip:
+    - "cutadapt"
+    upgrade: true
+  - type: "docker"
+    run:
+    - "cutadapt --version | sed 's/\\(.*\\)/cutadapt: \"\\1\"/' > /var/software_versions.txt\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/cutadapt/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/cutadapt"
+  executable: "target/executable/cutadapt/cutadapt"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/falco/.config.vsh.yaml

@@ -0,0 +1,347 @@
+name: "falco"
+version: "bump_viash_0_9_4"
+authors:
+- name: "Toni Verbeiren"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      github: "tverbeiren"
+      linkedin: "verbeiren"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Scientist and CEO"
+argument_groups:
+- name: "Input arguments"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "input fastq files"
+    info: null
+    example:
+    - "input1.fastq;input2.fastq"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+- name: "Run arguments"
+  arguments:
+  - type: "boolean_true"
+    name: "--nogroup"
+    description: "Disable grouping of bases for reads >50bp. \nAll reports will show\
+      \ data for every base in \nthe read. WARNING: When using this option, \nyour\
+      \ plots may end up a ridiculous size. You \nhave been warned!\n"
+    info: null
+    direction: "input"
+  - type: "file"
+    name: "--contaminents"
+    description: "Specifies a non-default file which contains \nthe list of contaminants\
+      \ to screen \noverrepresented sequences against. The file \nmust contain sets\
+      \ of named contaminants in \nthe form name[tab]sequence. Lines prefixed \nwith\
+      \ a hash will be ignored. Default: \nhttps://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/contaminant_list.txt\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--adapters"
+    description: "Specifies a non-default file which contains \nthe list of adapter\
+      \ sequences which will be \nexplicity searched against the library. The \nfile\
+      \ must contain sets of named adapters in \nthe form name[tab]sequence. Lines\
+      \ prefixed \nwith a hash will be ignored. Default:\nhttps://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/adapter_list.txt\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--limits"
+    description: "Specifies a non-default file which contains \na set of criteria\
+      \ which will be used to \ndetermine the warn/error limits for the \nvarious\
+      \ modules. This file can also be used \nto selectively remove some modules from\
+      \ the \noutput all together. The format needs to \nmirror the default limits.txt\
+      \ file found in \nthe Configuration folder. Default: \nhttps://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/limits.txt\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--subsample"
+    alternatives:
+    - "-s"
+    description: "[Falco only] makes falco faster (but \npossibly less accurate) by\
+      \ only processing \nreads that are a multiple of this value (using \n0-based\
+      \ indexing to number reads).\n"
+    info: null
+    example:
+    - 10
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--bisulfite"
+    alternatives:
+    - "-b"
+    description: "[Falco only] reads are whole genome \nbisulfite sequencing, and\
+      \ more Ts and fewer \nCs are therefore expected and will be \naccounted for\
+      \ in base content.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--reverse_complement"
+    alternatives:
+    - "-r"
+    description: "[Falco only] The input is a \nreverse-complement. All modules will\
+      \ be \ntested by swapping A/T and C/G\n"
+    info: null
+    direction: "input"
+- name: "Output arguments"
+  arguments:
+  - type: "file"
+    name: "--outdir"
+    alternatives:
+    - "-o"
+    description: "Create all output files in the specified \noutput directory. FALCO-SPECIFIC:\
+      \ If the \ndirectory does not exists, the program will \ncreate it.\n"
+    info: null
+    example:
+    - "output"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--format"
+    alternatives:
+    - "-f"
+    description: "Bypasses the normal sequence file format \ndetection and forces\
+      \ the program to use the \nspecified format. Validformats are bam, sam, \nbam_mapped,\
+      \ sam_mapped, fastq, fq, fastq.gz \nor fq.gz.\n"
+    info: null
+    required: false
+    choices:
+    - "bam"
+    - "sam"
+    - "bam_mapped"
+    - "sam_mapped"
+    - "fastq"
+    - "fq"
+    - "fastq.gz"
+    - "fq.gz"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--data_filename"
+    alternatives:
+    - "-D"
+    description: "[Falco only] Specify filename for FastQC \ndata output (TXT). If\
+      \ not specified, it will \nbe called fastq_data.txt in either the input \nfile's\
+      \ directory or the one specified in the \n--output flag. Only available when\
+      \ running \nfalco with a single input.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--report_filename"
+    alternatives:
+    - "-R"
+    description: "[Falco only] Specify filename for FastQC \nreport output (HTML).\
+      \ If not specified, it \nwill be called fastq_report.html in either \nthe input\
+      \ file's directory or the one \nspecified in the --output flag. Only \navailable\
+      \ when running falco with a single \ninput.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--summary_filename"
+    alternatives:
+    - "-S"
+    description: "[Falco only] Specify filename for the short \nsummary output (TXT).\
+      \ If not specified, it \nwill be called fastq_report.html in either \nthe input\
+      \ file's directory or the one \nspecified in the --output flag. Only \navailable\
+      \ when running falco with a single \ninput.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "A C++ drop-in replacement of FastQC to assess the quality of sequence\
+  \ read data"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "qc"
+- "fastqc"
+- "sequencing"
+license: "GPL-3.0"
+references:
+  doi:
+  - "10.12688/f1000research.21142.2"
+links:
+  repository: "https://github.com/smithlabcode/falco"
+  documentation: "https://falco.readthedocs.io/en/latest/"
+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:trixie-slim"
+  target_registry: "images.viash-hub.com"
+  target_tag: "bump_viash_0_9_4"
+  namespace_separator: "/"
+  setup:
+  - type: "apt"
+    packages:
+    - "wget"
+    - "build-essential"
+    - "g++"
+    - "zlib1g-dev"
+    - "procps"
+    interactive: false
+  - type: "docker"
+    run:
+    - "wget https://github.com/smithlabcode/falco/releases/download/v1.2.2/falco-1.2.2.tar.gz\
+      \ -O /tmp/falco.tar.gz && \\\ncd /tmp && \\\ntar xvf falco.tar.gz && \\\ncd\
+      \ falco-1.2.2 && \\\n./configure && \\\nmake all && \\\nmake install\n"
+  - type: "docker"
+    run:
+    - "echo \"falco: \\\"$(falco -v | sed -n 's/^falco //p')\\\"\" > /var/software_versions.txt\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/falco/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/falco"
+  executable: "target/executable/falco/falco"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/fastqc/.config.vsh.yaml

@@ -0,0 +1,370 @@
+name: "fastqc"
+version: "bump_viash_0_9_4"
+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"
+    description: "FASTQ file(s) to be analyzed.\n"
+    info: null
+    example:
+    - "input.fq"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+- name: "Outputs"
+  description: "At least one of the output options (--html, --zip, --summary, --data)\
+    \ must be used.\n"
+  arguments:
+  - type: "file"
+    name: "--html"
+    description: "Create the HTML report of the results. \n'*' wild card must be provided\
+      \ in the output file name. \nWild card will be replaced by the input file basename.\n\
+      e.g. \n  --input \"sample_1.fq\"\n  --html \"*.html\"\n  would create an output\
+      \ html file named sample_1.html\n"
+    info: null
+    example:
+    - "*.html"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: true
+    multiple_sep: ";"
+  - type: "file"
+    name: "--zip"
+    description: "Create the zip file(s) containing: html report, data, images, icons,\
+      \ summary, etc.\n'*' wild card must be provided in the output file name.\nWild\
+      \ card will be replaced by the input basename.\ne.g. \n  --input \"sample_1.fq\"\
+      \n  --html \"*.zip\"\n  would create an output zip file named sample_1.zip\n"
+    info: null
+    example:
+    - "*.zip"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: true
+    multiple_sep: ";"
+  - type: "file"
+    name: "--summary"
+    description: "Create the summary file(s).\n'*' wild card must be provided in the\
+      \ output file name.\nWild card will be replaced by the input basename.\ne.g.\
+      \ \n  --input \"sample_1.fq\"\n  --summary \"*_summary.txt\"\n  would create\
+      \ an output summary.txt file named sample_1_summary.txt\n"
+    info: null
+    example:
+    - "*_summary.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: true
+    multiple_sep: ";"
+  - type: "file"
+    name: "--data"
+    description: "Create the data file(s).\n'*' wild card must be provided in the\
+      \ output file name.\nWild card will be replaced by the input basename.\ne.g.\
+      \ \n  --input \"sample_1.fq\"\n  --summary \"*_data.txt\"\n  would create an\
+      \ output data.txt file named sample_1_data.txt\n"
+    info: null
+    example:
+    - "*_data.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: true
+    multiple_sep: ";"
+- name: "Options"
+  arguments:
+  - type: "boolean_true"
+    name: "--casava"
+    description: "Files come from raw casava output. Files in the same sample\ngroup\
+      \ (differing only by the group number) will be analysed\nas a set rather than\
+      \ individually. Sequences with the filter\nflag set in the header will be excluded\
+      \ from the analysis.\nFiles must have the same names given to them by casava\n\
+      (including being gzipped and ending with .gz) otherwise they\nwon't be grouped\
+      \ together correctly.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--nano"
+    description: "Files come from nanopore sequences and are in fast5 format. In\n\
+      this mode you can pass in directories to process and the program\nwill take\
+      \ in all fast5 files within those directories and produce\na single output file\
+      \ from the sequences found in all files.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--nofilter"
+    description: "If running with --casava then don't remove read flagged by\ncasava\
+      \ as poor quality when performing the QC analysis.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--nogroup"
+    description: "Disable grouping of bases for reads >50bp. \nAll reports will show\
+      \ data for every base in the read. \nWARNING: Using this option will cause fastqc\
+      \ to crash \nand burn if you use it on really long reads, and your \nplots may\
+      \ end up a ridiculous size. You have been warned!\n"
+    info: null
+    direction: "input"
+  - type: "integer"
+    name: "--min_length"
+    description: "Sets an artificial lower limit on the length of the \nsequence to\
+      \ be shown in the report. As long as you \nset this to a value greater or equal\
+      \ to your longest \nread length then this will be the sequence length used \n\
+      to create your read groups. This can be useful for making\ndirectly comparable\
+      \ statistics from datasets with somewhat \nvariable read lengths.\n"
+    info: null
+    example:
+    - 0
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--format"
+    alternatives:
+    - "-f"
+    description: "Bypasses the normal sequence file format detection and \nforces\
+      \ the program to use the specified format. \nValid formats are bam, sam, bam_mapped,\
+      \ sam_mapped, and fastq.\n"
+    info: null
+    example:
+    - "bam"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--contaminants"
+    alternatives:
+    - "-c"
+    description: "Specifies a non-default file which contains the list \nof contaminants\
+      \ to screen overrepresented sequences against. \nThe file must contain sets\
+      \ of named contaminants in the form\nname[tab]sequence. Lines prefixed with\
+      \ a hash will be ignored.\n"
+    info: null
+    example:
+    - "contaminants.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--adapters"
+    alternatives:
+    - "-a"
+    description: "Specifies a non-default file which contains the list of \nadapter\
+      \ sequences which will be explicitly searched against \nthe library. The file\
+      \ must contain sets of named adapters \nin the form name[tab]sequence. Lines\
+      \ prefixed with a hash will be ignored.\n"
+    info: null
+    example:
+    - "adapters.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--limits"
+    alternatives:
+    - "-l"
+    description: "Specifies a non-default file which contains \na set of criteria\
+      \ which will be used to determine \nthe warn/error limits for the various modules.\
+      \ \nThis file can also be used to selectively remove \nsome modules from the\
+      \ output altogether. The format \nneeds to mirror the default limits.txt file\
+      \ found in \nthe Configuration folder.\n"
+    info: null
+    example:
+    - "limits.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--kmers"
+    alternatives:
+    - "-k"
+    description: "Specifies the length of Kmer to look for in the Kmer \ncontent module.\
+      \ Specified Kmer length must be between \n2 and 10. Default length is 7 if not\
+      \ specified.\n"
+    info: null
+    example:
+    - 7
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--quiet"
+    alternatives:
+    - "-q"
+    description: "Suppress all progress messages on stdout and only report errors.\n"
+    info: null
+    direction: "input"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "FastQC - A high throughput sequence QC analysis tool."
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "Quality control"
+- "BAM"
+- "SAM"
+- "FASTQ"
+license: "GPL-3.0, Apache-2.0"
+links:
+  repository: "https://github.com/s-andrews/FastQC"
+  homepage: "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/"
+  documentation: "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/"
+  issue_tracker: "https://github.com/s-andrews/FastQC/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: "biocontainers/fastqc:v0.11.9_cv8"
+  target_registry: "images.viash-hub.com"
+  target_tag: "bump_viash_0_9_4"
+  namespace_separator: "/"
+  setup:
+  - type: "docker"
+    run:
+    - "echo \"fastqc: $(fastqc --version | sed -n 's/^FastQC //p')\" > /var/software_versions.txt\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/fastqc/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/fastqc"
+  executable: "target/executable/fastqc/fastqc"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/featurecounts/.config.vsh.yaml

@@ -0,0 +1,675 @@
+name: "featurecounts"
+version: "bump_viash_0_9_4"
+authors:
+- name: "Sai Nirmayi Yasa"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "nirmayi@data-intuitive.com"
+      github: "sainirmayi"
+      linkedin: "sai-nirmayi-yasa"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Junior Bioinformatics Researcher"
+argument_groups:
+- name: "Inputs"
+  arguments:
+  - type: "file"
+    name: "--annotation"
+    alternatives:
+    - "-a"
+    description: "Name of an annotation file. GTF/GFF format by default. See '--format'\
+      \ option for more format information.\n"
+    info: null
+    example:
+    - "annotation.gtf"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--input"
+    alternatives:
+    - "-i"
+    description: "A list of SAM or BAM format files separated by semi-colon (;). They\
+      \ can be either name or location sorted. Location-sorted paired-end reads are\
+      \ automatically sorted by read names.\n"
+    info: null
+    example:
+    - "input_file1.bam"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--counts"
+    alternatives:
+    - "-o"
+    description: "Name of output file including read counts in tab delimited format.\n"
+    info: null
+    example:
+    - "features.tsv"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--summary"
+    description: "Summary statistics of counting results in tab delimited format.\n"
+    info: null
+    example:
+    - "summary.tsv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--junctions"
+    description: "Count number of reads supporting each exon-exon junction. Junctions\
+      \ were identified from those exon-spanning reads in the input (containing 'N'\
+      \ in CIGAR string).\n"
+    info: null
+    example:
+    - "junctions.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Annotation"
+  arguments:
+  - type: "string"
+    name: "--format"
+    alternatives:
+    - "-F"
+    description: "Specify format of the provided annotation file. Acceptable formats\
+      \ include 'GTF' (or compatible GFF format) and 'SAF'. 'GTF' by default. \n"
+    info: null
+    example:
+    - "GTF"
+    required: false
+    choices:
+    - "GTF"
+    - "GFF"
+    - "SAF"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--feature_type"
+    alternatives:
+    - "-t"
+    description: "Specify feature type(s) in a GTF annotation. If multiple types are\
+      \ provided, they should be separated by ';' with no space in between. 'exon'\
+      \ by default. Rows in the annotation with a matched feature will be extracted\
+      \ and used for read mapping.\n"
+    info: null
+    example:
+    - "exon"
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+  - type: "string"
+    name: "--attribute_type"
+    alternatives:
+    - "-g"
+    description: "Specify attribute type in GTF annotation. 'gene_id' by default.\
+      \ Meta-features used for read counting will be extracted from annotation using\
+      \ the provided value.\n"
+    info: null
+    example:
+    - "gene_id"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--extra_attributes"
+    description: "Extract extra attribute types from the provided GTF annotation and\
+      \ include them in the counting output. These attribute types will not be used\
+      \ to group features. If more than one attribute type is provided they should\
+      \ be separated by semicolon (;).\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+  - type: "file"
+    name: "--chrom_alias"
+    alternatives:
+    - "-A"
+    description: "Provide a chromosome name alias file to match chr names in annotation\
+      \ with those in the reads. This should be a two-column comma-delimited text\
+      \ file. Its first column should include chr names in the annotation and its\
+      \ second column should include chr names in the reads. Chr names are case sensitive.\
+      \ No column header should be included in the file.\n"
+    info: null
+    example:
+    - "chrom_alias.csv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Level of summarization"
+  arguments:
+  - type: "boolean_true"
+    name: "--feature_level"
+    alternatives:
+    - "-f"
+    description: "Perform read counting at feature level (eg. counting reads for exons\
+      \ rather than genes).\n"
+    info: null
+    direction: "input"
+- name: "Overlap between reads and features"
+  arguments:
+  - type: "boolean_true"
+    name: "--overlapping"
+    alternatives:
+    - "-O"
+    description: "Assign reads to all their overlapping meta-features (or features\
+      \ if '--feature_level' is specified).\n"
+    info: null
+    direction: "input"
+  - type: "integer"
+    name: "--min_overlap"
+    description: "Minimum number of overlapping bases in a read that is required for\
+      \ read assignment. 1 by default. Number of overlapping bases is counted from\
+      \ both reads if paired end. If a negative value is provided, then a gap of up\
+      \ to specified size will be allowed between read and the feature that the read\
+      \ is assigned to.\n"
+    info: null
+    example:
+    - 1
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "double"
+    name: "--frac_overlap"
+    description: "Minimum fraction of overlapping bases in a read that is required\
+      \ for read assignment. Value should be within range [0,1]. 0 by default. Number\
+      \ of overlapping bases is counted from both reads if paired end. Both this option\
+      \ and '--min_overlap' option need to be satisfied for read assignment.\n"
+    info: null
+    example:
+    - 0.0
+    required: false
+    min: 0.0
+    max: 1.0
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "double"
+    name: "--frac_overlap_feature"
+    description: "Minimum fraction of overlapping bases in a feature that is required\
+      \ for read assignment. Value should be within range [0,1]. 0 by default.\n"
+    info: null
+    example:
+    - 0.0
+    required: false
+    min: 0.0
+    max: 1.0
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--largest_overlap"
+    description: "Assign reads to a meta-feature/feature that has the largest number\
+      \ of overlapping bases.\n"
+    info: null
+    direction: "input"
+  - type: "integer"
+    name: "--non_overlap"
+    description: "Maximum number of non-overlapping bases in a read (or a read pair)\
+      \ that is allowed when being assigned to a feature. No limit is set by default.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--non_overlap_feature"
+    description: "Maximum number of non-overlapping bases in a feature that is allowed\
+      \ in read assignment. No limit is set by default.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--read_extension5"
+    description: "Reads are extended upstream by <int> bases from their 5' end.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--read_extension3"
+    description: "Reads are extended upstream by <int> bases from their 3' end.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--read2pos"
+    description: "Reduce reads to their 5' most base or 3' most base. Read counting\
+      \ is then performed based on the single base the read is reduced to.\n"
+    info: null
+    required: false
+    choices:
+    - 3
+    - 5
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Multi-mapping reads"
+  arguments:
+  - type: "boolean_true"
+    name: "--multi_mapping"
+    alternatives:
+    - "-M"
+    description: "Multi-mapping reads will also be counted. For a multi-mapping read,\
+      \ all its reported alignments will be counted. The 'NH' tag in BAM/SAM input\
+      \ is used to detect multi-mapping reads.\n"
+    info: null
+    direction: "input"
+- name: "Fractional counting"
+  arguments:
+  - type: "boolean_true"
+    name: "--fraction"
+    description: "Assign fractional counts to features. This option must be used together\
+      \ with '--multi_mapping' or '--overlapping' or both. When '--multi_mapping'\
+      \ is specified, each reported alignment from a multi-mapping read (identified\
+      \ via 'NH' tag) will carry a fractional count of 1/x, instead of 1 (one), where\
+      \ x is the total number of alignments reported for the same read. When '--overlapping'\
+      \ is specified, each overlapping feature will receive a fractional count of\
+      \ 1/y, where y is the total number of features overlapping with the read. When\
+      \ both '--multi_mapping' and '--overlapping' are specified, each alignment will\
+      \ carry a fractional count of 1/(x*y).\n"
+    info: null
+    direction: "input"
+- name: "Read filtering"
+  arguments:
+  - type: "integer"
+    name: "--min_map_quality"
+    alternatives:
+    - "-Q"
+    description: "The minimum mapping quality score a read must satisfy in order to\
+      \ be counted. For paired-end reads, at least one end should satisfy this criteria.\
+      \ 0 by default.\n"
+    info: null
+    example:
+    - 0
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--split_only"
+    description: "Count split alignments only (ie. alignments with CIGAR string containing\
+      \ 'N'). An example of split alignments is exon-spanning reads in RNA-seq data.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--non_split_only"
+    description: "If specified, only non-split alignments (CIGAR strings do not contain\
+      \ letter 'N') will be counted. All the other alignments will be ignored.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--primary"
+    description: "Count primary alignments only. Primary alignments are identified\
+      \ using bit 0x100 in SAM/BAM FLAG field.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--ignore_dup"
+    description: "Ignore duplicate reads in read counting. Duplicate reads are identified\
+      \ using bit Ox400 in BAM/SAM FLAG field. The whole read pair is ignored if one\
+      \ of the reads is a duplicate read for paired end data.\n"
+    info: null
+    direction: "input"
+- name: "Strandedness"
+  arguments:
+  - type: "integer"
+    name: "--strand"
+    alternatives:
+    - "-s"
+    description: "Perform strand-specific read counting. A single integer value (applied\
+      \ to all input files) should be provided. Possible values include: 0 (unstranded),\
+      \ 1 (stranded) and 2 (reversely stranded). Default value is 0 (ie. unstranded\
+      \ read counting carried out for all input files).\n"
+    info: null
+    example:
+    - 0
+    required: false
+    choices:
+    - 0
+    - 1
+    - 2
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Exon-exon junctions"
+  arguments:
+  - type: "file"
+    name: "--ref_fasta"
+    alternatives:
+    - "-G"
+    description: "Provide the name of a FASTA-format file that contains the reference\
+      \ sequences used in read mapping that produced the provided SAM/BAM files.\n"
+    info: null
+    example:
+    - "reference.fasta"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Parameters specific to paired end reads"
+  arguments:
+  - type: "boolean_true"
+    name: "--paired"
+    alternatives:
+    - "-p"
+    description: "Specify that input data contain paired-end reads. To perform fragment\
+      \ counting (ie. counting read pairs), the '--countReadPairs' parameter should\
+      \ also be specified in addition to this parameter.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--count_read_pairs"
+    description: "Count read pairs (fragments) instead of reads. This option is only\
+      \ applicable for paired-end reads.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--both_aligned"
+    alternatives:
+    - "-B"
+    description: "Count read pairs (fragments) instead of reads. This option is only\
+      \ applicable for paired-end reads.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--check_pe_dist"
+    alternatives:
+    - "-P"
+    description: "Check validity of paired-end distance when counting read pairs.\
+      \ Use '--min_length' and '--max_length' to set thresholds.\n"
+    info: null
+    direction: "input"
+  - type: "integer"
+    name: "--min_length"
+    alternatives:
+    - "-d"
+    description: "Minimum fragment/template length, 50 by default.\n"
+    info: null
+    example:
+    - 50
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--max_length"
+    alternatives:
+    - "-D"
+    description: "Maximum fragment/template length, 600 by default.\n"
+    info: null
+    example:
+    - 600
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--same_strand"
+    alternatives:
+    - "-C"
+    description: "Do not count read pairs that have their two ends mapping to different\
+      \ chromosomes or mapping to same chromosome but on different strands.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--donotsort"
+    description: "Do not sort reads in BAM/SAM input. Note that reads from the same\
+      \ pair are required to be located next to each other in the input.\n"
+    info: null
+    direction: "input"
+- name: "Read groups"
+  arguments:
+  - type: "boolean_true"
+    name: "--by_read_group"
+    description: "Assign reads by read group. \"RG\" tag is required to be present\
+      \ in the input BAM/SAM files.\n"
+    info: null
+    direction: "input"
+- name: "Long reads"
+  arguments:
+  - type: "boolean_true"
+    name: "--long_reads"
+    description: "Count long reads such as Nanopore and PacBio reads. Long read counting\
+      \ can only run in one thread and only reads (not read-pairs) can be counted.\
+      \ There is no limitation on the number of 'M' operations allowed in a CIGAR\
+      \ string in long read counting.\n"
+    info: null
+    direction: "input"
+- name: "Assignment results for each read"
+  arguments:
+  - type: "file"
+    name: "--detailed_results"
+    description: "Directory to save the detailed assignment results. Use `--detailed_results_format`\
+      \ to determine the format of the detailed results.\n"
+    info: null
+    example:
+    - "detailed_results"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--detailed_results_format"
+    alternatives:
+    - "-R"
+    description: "Output detailed assignment results for each read or read-pair. Results\
+      \ are saved to a file that is in one of the following formats: CORE, SAM and\
+      \ BAM. See documentaiton for more info about these formats.\n"
+    info: null
+    required: false
+    choices:
+    - "CORE"
+    - "SAM"
+    - "BAM"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Miscellaneous"
+  arguments:
+  - type: "integer"
+    name: "--max_M_op"
+    description: "Maximum number of 'M' operations allowed in a CIGAR string. 10 by\
+      \ default. Both 'X' and '=' are treated as 'M' and adjacent 'M' operations are\
+      \ merged in the CIGAR string.\n"
+    info: null
+    example:
+    - 10
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--verbose"
+    description: "Output verbose information for debugging, such as un-matched chromosome/contig\
+      \ names.\n"
+    info: null
+    direction: "input"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "featureCounts is a read summarization program for counting reads generated\
+  \ from either RNA or genomic DNA sequencing experiments by implementing highly efficient\
+  \ chromosome hashing and feature blocking techniques. It works with either single\
+  \ or paired-end reads and provides a wide range of options appropriate for different\
+  \ sequencing applications.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test_data"
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "Read counting"
+- "Genomic features"
+license: "GPL-3.0"
+references:
+  doi:
+  - "10.1093/bioinformatics/btt656"
+links:
+  repository: "https://github.com/ShiLab-Bioinformatics/subread"
+  homepage: "https://subread.sourceforge.net/"
+  documentation: "https://subread.sourceforge.net/SubreadUsersGuide.pdf"
+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/subread:2.0.6--he4a0461_0"
+  target_registry: "images.viash-hub.com"
+  target_tag: "bump_viash_0_9_4"
+  namespace_separator: "/"
+  setup:
+  - type: "docker"
+    run:
+    - "featureCounts -v 2>&1 | sed 's/featureCounts v\\([0-9.]*\\)/featureCounts:\
+      \ \\1/' > /var/software_versions.txt\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/featurecounts/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/featurecounts"
+  executable: "target/executable/featurecounts/featurecounts"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/fq_subsample/.config.vsh.yaml

@@ -0,0 +1,220 @@
+name: "fq_subsample"
+version: "bump_viash_0_9_4"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--input_1"
+    description: "First input fastq file to subsample. Accepts both raw and gzipped\
+      \ FASTQ inputs."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--input_2"
+    description: "Second input fastq files to subsample. Accepts both raw and gzipped\
+      \ FASTQ inputs."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--output_1"
+    description: "Sampled read 1 fastq files. Output will be gzipped if ends in `.gz`."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_2"
+    description: "Sampled read 2 fastq files. Output will be gzipped if ends in `.gz`."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Options"
+  arguments:
+  - type: "double"
+    name: "--probability"
+    description: "The probability a record is kept, as a percentage (0.0, 1.0). Cannot\
+      \ be used with `record-count`"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--record_count"
+    description: "The exact number of records to keep. Cannot be used with `probability`"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--seed"
+    description: "Seed to use for the random number generator"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "fq subsample outputs a subset of records from single or paired FASTQ\
+  \ files."
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test_data"
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "fastq"
+- "subsample"
+- "subset"
+license: "MIT"
+links:
+  repository: "https://github.com/stjude-rust-labs/fq"
+  homepage: "https://github.com/stjude-rust-labs/fq/blob/master/README.md"
+  documentation: "https://github.com/stjude-rust-labs/fq/blob/master/README.md"
+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: "rust:1.81-slim"
+  target_registry: "images.viash-hub.com"
+  target_tag: "bump_viash_0_9_4"
+  namespace_separator: "/"
+  setup:
+  - type: "docker"
+    run:
+    - "apt-get update && apt-get install -y git procps && \\\ngit clone --depth 1\
+      \ --branch v0.12.0 https://github.com/stjude-rust-labs/fq.git && \\\ncd fq &&\
+      \ \\\ncargo install --locked --path . && \\\nmv target/release/fq /usr/local/bin/\
+      \ && \\\ncd / && rm -rf /fq\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/fq_subsample/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/fq_subsample"
+  executable: "target/executable/fq_subsample/fq_subsample"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/gffread/.config.vsh.yaml

@@ -0,0 +1,715 @@
+name: "gffread"
+version: "bump_viash_0_9_4"
+authors:
+- name: "Emma Rousseau"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "emma@data-intuitive.com"
+      github: "emmarousseau"
+      linkedin: "emmarousseau1"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Bioinformatician"
+argument_groups:
+- name: "Inputs"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "A reference file in either the GFF3, GFF2 or GTF format.\n"
+    info: null
+    example:
+    - "annotation.gff"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--chr_mapping"
+    alternatives:
+    - "-m"
+    description: "<chr_replace> is a name mapping table for converting reference sequence\
+      \ names, \nhaving this 2-column format: <original_ref_ID> <new_ref_ID>.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--seq_info"
+    alternatives:
+    - "-s"
+    description: "<seq_info.fsize> is a tab-delimited file providing this info for\
+      \ each of the mapped \nsequences: <seq-name> <seq-length> <seq-description>\
+      \ (useful for --description option with \nmRNA/EST/protein mappings).\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--genome"
+    alternatives:
+    - "-g"
+    description: "Full path to a multi-fasta file with the genomic sequences for all\
+      \ input mappings, \nOR a directory with single-fasta files (one per genomic\
+      \ sequence, with file names \nmatching sequence names).\n"
+    info: null
+    example:
+    - "genome.fa"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--outfile"
+    alternatives:
+    - "-o"
+    description: "Write the output records into <outfile>.\n"
+    info: null
+    example:
+    - "output.gff"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--force_exons"
+    description: "Make sure that the lowest level GFF features are considered \"exon\"\
+      \ features.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--gene2exon"
+    description: "For single-line genes not parenting any transcripts, add an exon\
+      \ feature spanning \nthe entire gene (treat it as a transcript).\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--t_adopt"
+    description: "Try to find a parent gene overlapping/containing a transcript that\
+      \ does not have \nany explicit gene Parent.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--decode"
+    alternatives:
+    - "-D"
+    description: "Decode url encoded characters within attributes.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--merge_exons"
+    alternatives:
+    - "-Z"
+    description: "Merge very close exons into a single exon (when intron size<4).\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--junctions"
+    alternatives:
+    - "-j"
+    description: "Output the junctions and the corresponding transcripts.\n"
+    info: null
+    direction: "input"
+  - type: "file"
+    name: "--spliced_exons"
+    alternatives:
+    - "-w"
+    description: "Write a fasta file with spliced exons for each transcript.\n"
+    info: null
+    example:
+    - "exons.fa"
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--w_add"
+    description: "For the --spliced_exons option, extract additional <N> bases both\
+      \ upstream and \ndownstream of the transcript boundaries.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--w_nocds"
+    description: "For --spliced_exons, disable the output of CDS info in the FASTA\
+      \ file.\n"
+    info: null
+    direction: "input"
+  - type: "file"
+    name: "--spliced_cds"
+    alternatives:
+    - "-x"
+    description: "Write a fasta file with spliced CDS for each GFF transcript.\n"
+    info: null
+    example:
+    - "cds.fa"
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--tr_cds"
+    alternatives:
+    - "-y"
+    description: "Write a protein fasta file with the translation of CDS for each\
+      \ record.\n"
+    info: null
+    example:
+    - "tr_cds.fa"
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--w_coords"
+    alternatives:
+    - "-W"
+    description: "For --spliced_exons, --spliced_cds and -tr_cds options, write in\
+      \ the FASTA defline \nall the exon coordinates projected onto the spliced sequence.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--stop_dot"
+    alternatives:
+    - "-S"
+    description: "For --tr_cds option, use '*' instead of '.' as stop codon translation.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--id_version"
+    alternatives:
+    - "-L"
+    description: "Ensembl GTF to GFF3 conversion, adds version to IDs.\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--trackname"
+    alternatives:
+    - "-t"
+    description: "Use <trackname> in the 2nd column of each GFF/GTF output line.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--gtf_output"
+    alternatives:
+    - "-T"
+    description: "Main output will be GTF instead of GFF3.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--bed"
+    description: "Output records in BED format instead of default GFF3.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--tlf"
+    description: "Output \"transcript line format\" which is like GFF but with exons\
+      \ and CDS related \nfeatures stored as GFF attributes in the transcript feature\
+      \ line, like this:\n  exoncount=N;exons=<exons>;CDSphase=<N>;CDS=<CDScoords>\n\
+      <exons> is a comma-delimited list of exon_start-exon_end coordinates;\n<CDScoords>\
+      \ is CDS_start:CDS_end coordinates or a list like <exons>.\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--table"
+    description: "Output a simple tab delimited format instead of GFF, with columns\
+      \ having the values \nof GFF attributes given in <attrlist>; special pseudo-attributes\
+      \ (prefixed by @) are \nrecognized:\n  @id, @geneid, @chr, @start, @end, @strand,\
+      \ @numexons, @exons, @cds, @covlen, @cdslen\nIf any of --spliced_exons/--tr_cds/--spliced_cds\
+      \ FASTA output files are enabled, the \nsame fields (excluding @id) are appended\
+      \ to the definition line of corresponding FASTA\nrecords.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--expose_dups"
+    alternatives:
+    - "-E"
+    - "-v"
+    description: "Expose (warn about) duplicate transcript IDs and other potential\
+      \ problems with the \ngiven GFF/GTF records.\n"
+    info: null
+    direction: "input"
+- name: "Options"
+  arguments:
+  - type: "file"
+    name: "--ids"
+    description: "Discard records/transcripts if their IDs are not listed in <IDs.lst>.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--nids"
+    description: "Discard records/transcripts if their IDs are listed in <IDs.lst>.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--maxintron"
+    alternatives:
+    - "-i"
+    description: "Discard transcripts having an intron larger than <maxintron>.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--minlen"
+    alternatives:
+    - "-l"
+    description: "Discard transcripts shorter than <minlen> bases.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--range"
+    alternatives:
+    - "-r"
+    description: "Only show transcripts overlapping coordinate range <start>..<end>\
+      \ (on chromosome/contig \n<chr>, strand <strand> if provided).\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--strict_range"
+    alternatives:
+    - "-R"
+    description: "For --range option, discard all transcripts that are not fully contained\
+      \ within the given \nrange.\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--jmatch"
+    description: "Only output transcripts matching the given junction.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--no_single_exon"
+    alternatives:
+    - "-U"
+    description: "Discard single-exon transcripts.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--coding"
+    alternatives:
+    - "-C"
+    description: "Coding only: discard mRNAs that have no CDS features.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--nc"
+    description: "Non-coding only: discard mRNAs that have CDS features.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--ignore_locus"
+    description: "Discard locus features and attributes found in the input.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--description"
+    alternatives:
+    - "-A"
+    description: "Use the description field from <seq_info.fsize> and add it as the\
+      \ value for a 'descr' \nattribute to the GFF record.\n"
+    info: null
+    direction: "input"
+- name: "Sorting"
+  arguments:
+  - type: "boolean_true"
+    name: "--sort_alpha"
+    description: "Chromosomes (reference sequences) are sorted alphabetically.\n"
+    info: null
+    direction: "input"
+  - type: "file"
+    name: "--sort_by"
+    description: "Sort the reference sequences by the order in which their names are\
+      \ given in the \n<refseq.lst> file.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Misc options"
+  arguments:
+  - type: "boolean_true"
+    name: "--keep_attrs"
+    alternatives:
+    - "-F"
+    description: "Keep all GFF attributes (for non-exon features).\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--keep_exon_attrs"
+    description: "For -F option, do not attempt to reduce redundant exon/CDS attributes.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_exon_attrs"
+    alternatives:
+    - "-G"
+    description: "Do not keep exon attributes, move them to the transcript feature\
+      \ (for GFF3 output).\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--attrs"
+    description: "Only output the GTF/GFF attributes listed in <attr-list> which is\
+      \ a comma delimited \nlist of attribute names to.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--keep_genes"
+    description: "In transcript-only mode (default), also preserve gene records.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--keep_comments"
+    description: "For GFF3 input/output, try to preserve comments.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--process_other"
+    alternatives:
+    - "-O"
+    description: "process other non-transcript GFF records (by default non-transcript\
+      \ records are ignored).\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--rm_stop_codons"
+    alternatives:
+    - "-V"
+    description: "Discard any mRNAs with CDS having in-frame stop codons (requires\
+      \ --genome).\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--adj_cds_start"
+    alternatives:
+    - "-H"
+    description: "For --rm_stop_codons option, check and adjust the starting CDS phase\
+      \ if the original phase\nleads to a translation with an in-frame stop codon.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--opposite_strand"
+    alternatives:
+    - "-B"
+    description: "For -V option, single-exon transcripts are also checked on the opposite\
+      \ strand (requires \n--genome).  \n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--coding_status"
+    alternatives:
+    - "-P"
+    description: "Add transcript level GFF attributes about the coding status of each\
+      \ transcript, including \npartialness or in-frame stop codons (requires --genome).\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--add_hasCDS"
+    description: "Add a \"hasCDS\" attribute with value \"true\" for transcripts that\
+      \ have CDS features. \n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--adj_stop"
+    description: "Stop codon adjustment: enables --coding_status and performs automatic\
+      \ adjustment of the CDS stop \ncoordinate if premature or downstream.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--rm_noncanon"
+    alternatives:
+    - "-N"
+    description: "Discard multi-exon mRNAs that have any intron with a non-canonical\
+      \ splice site consensus \n(i.e. not GT-AG, GC-AG or AT-AC).\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--complete_cds"
+    alternatives:
+    - "-J"
+    description: "Discard any mRNAs that either lack initial START codon or the terminal\
+      \ STOP codon, or \nhave an in-frame stop codon (i.e. only print mRNAs with a\
+      \ complete CDS).\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_pseudo"
+    description: "Filter out records matching the 'pseudo' keyword.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--in_bed"
+    description: "Input should be parsed as BED format (automatic if the input filename\
+      \ ends with .bed*).\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--in_tlf"
+    description: "Input GFF-like one-line-per-transcript format without exon/CDS features\
+      \ (see --tlf option \nbelow); automatic if the input filename ends with .tlf).\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--stream"
+    description: "Fast processing of input GFF/BED transcripts as they are received\
+      \ (no sorting, exons must \nbe grouped by transcript in the input data).\n"
+    info: null
+    direction: "input"
+- name: "Clustering"
+  arguments:
+  - type: "boolean_true"
+    name: "--merge"
+    alternatives:
+    - "-M"
+    description: "Cluster the input transcripts into loci, discarding \"redundant\"\
+      \ transcripts (those with \nthe same exact introns and fully contained or equal\
+      \ boundaries).\n"
+    info: null
+    direction: "input"
+  - type: "file"
+    name: "--dupinfo"
+    alternatives:
+    - "-d"
+    description: "For --merge option, write duplication info to file <dupinfo>.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--cluster_only"
+    description: "Same as --merge but without discarding any of the \"duplicate\"\
+      \ transcripts, only create \n\"locus\" features.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--rm_redundant"
+    alternatives:
+    - "-K"
+    description: "For --merge option: also discard as redundant the shorter, fully\
+      \ contained transcripts (intron \nchains matching a part of the container).\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_boundary"
+    alternatives:
+    - "-Q"
+    description: "For --merge option, no longer require boundary containment when\
+      \ assessing redundancy (can be \ncombined with --rm_redundant); only introns\
+      \ have to match for multi-exon transcripts, and >=80%\noverlap for single-exon\
+      \ transcripts.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_overlap"
+    alternatives:
+    - "-Y"
+    description: "For --merge option, enforce --no_boundary but also discard overlapping\
+      \ single-exon transcripts,\neven on the opposite strand (can be combined with\
+      \ --rm_redudant).\n"
+    info: null
+    direction: "input"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Validate, filter, convert and perform various other operations on GFF\
+  \ files."
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test_data"
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "gff"
+- "conversion"
+- "validation"
+- "filtering"
+license: "MIT"
+references:
+  doi:
+  - "10.12688/f1000research.23297.2"
+links:
+  repository: "https://github.com/gpertea/gffread"
+  homepage: "https://ccb.jhu.edu/software/stringtie/gff.shtml#gffread"
+  documentation: "https://ccb.jhu.edu/software/stringtie/gff.shtml#gffread"
+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/gffread:0.12.7--hdcf5f25_3"
+  target_registry: "images.viash-hub.com"
+  target_tag: "bump_viash_0_9_4"
+  namespace_separator: "/"
+  setup:
+  - type: "docker"
+    run:
+    - "echo \"gffread: \\\"$(gffread --version 2>&1)\\\"\" > /var/software_versions.txt\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/gffread/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/gffread"
+  executable: "target/executable/gffread/gffread"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/kallisto/kallisto_index/.config.vsh.yaml

@@ -0,0 +1,248 @@
+name: "kallisto_index"
+namespace: "kallisto"
+version: "bump_viash_0_9_4"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "Path to a FASTA-file containing the transcriptome sequences, either\
+      \ in plain text or \ncompressed (.gz) format.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--d_list"
+    description: "Path to a FASTA-file containing sequences to mask from quantification.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--index"
+    info: null
+    example:
+    - "Kallisto_index"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Options"
+  arguments:
+  - type: "integer"
+    name: "--kmer_size"
+    description: "Kmer length passed to indexing step of pseudoaligners (default:\
+      \ '31').\n"
+    info: null
+    example:
+    - 31
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--make_unique"
+    description: "Replace repeated target names with unique names.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--aa"
+    description: "Generate index from a FASTA-file containing amino acid sequences.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--distiguish"
+    description: "Generate index where sequences are distinguished by the sequence\
+      \ names.\n"
+    info: null
+    direction: "input"
+  - type: "integer"
+    name: "--min_size"
+    alternatives:
+    - "-m"
+    description: "Length of minimizers (default: automatically chosen).\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--ec_max_size"
+    alternatives:
+    - "-e"
+    description: "Maximum number of targets in an equivalence class (default: no maximum).\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--tmp"
+    alternatives:
+    - "-T"
+    description: "Path to a directory for temporary files.\n"
+    info: null
+    example:
+    - "tmp"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Build a Kallisto index for the transcriptome to use Kallisto in the\
+  \ mapping-based mode.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test_data"
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "kallisto"
+- "index"
+license: "BSD 2-Clause License"
+references:
+  doi:
+  - "https://doi.org/10.1038/nbt.3519"
+links:
+  repository: "https://github.com/pachterlab/kallisto"
+  homepage: "https://pachterlab.github.io/kallisto/about"
+  documentation: "https://pachterlab.github.io/kallisto/manual"
+  issue_tracker: "https://github.com/pachterlab/kallisto/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: "ubuntu:22.04"
+  target_registry: "images.viash-hub.com"
+  target_tag: "bump_viash_0_9_4"
+  namespace_separator: "/"
+  setup:
+  - type: "docker"
+    run:
+    - "apt-get update && \\\napt-get install -y --no-install-recommends wget && \\\
+      \nwget --no-check-certificate https://github.com/pachterlab/kallisto/releases/download/v0.50.1/kallisto_linux-v0.50.1.tar.gz\
+      \ && \\\ntar -xzf kallisto_linux-v0.50.1.tar.gz && \\\nmv kallisto/kallisto\
+      \ /usr/local/bin/\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/kallisto/kallisto_index/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/kallisto/kallisto_index"
+  executable: "target/executable/kallisto/kallisto_index/kallisto_index"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/kallisto/kallisto_quant/.config.vsh.yaml

@@ -0,0 +1,276 @@
+name: "kallisto_quant"
+namespace: "kallisto"
+version: "bump_viash_0_9_4"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "List of input FastQ files of size 1 and 2 for single-end and paired-end\
+      \ data, respectively."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+  - type: "file"
+    name: "--index"
+    alternatives:
+    - "-i"
+    description: "Kallisto genome index."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--output_dir"
+    alternatives:
+    - "-o"
+    description: "Directory to write output to."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--log"
+    description: "File containing log information from running kallisto quant"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Options"
+  arguments:
+  - type: "boolean_true"
+    name: "--single"
+    description: "Single end mode."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--single_overhang"
+    description: "Include reads where unobserved rest of fragment is predicted to\
+      \ lie outside a transcript."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--fr_stranded"
+    description: "Strand specific reads, first read forward."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--rf_stranded"
+    description: "Strand specific reads, first read reverse."
+    info: null
+    direction: "input"
+  - type: "double"
+    name: "--fragment_length"
+    alternatives:
+    - "-l"
+    description: "The estimated average fragment length."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "double"
+    name: "--sd"
+    alternatives:
+    - "-s"
+    description: "The estimated standard deviation of the fragment length (default:\
+      \ -l, -s values are estimated \nfrom paired end data, but are required when\
+      \ using --single).\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--plaintext"
+    description: "Output plaintext instead of HDF5."
+    info: null
+    direction: "input"
+  - type: "integer"
+    name: "--bootstrap_samples"
+    alternatives:
+    - "-b"
+    description: "Number of bootstrap samples to draw. Default: '0'\n"
+    info: null
+    example:
+    - 0
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--seed"
+    description: "Random seed for bootstrap. Default: '42'\n"
+    info: null
+    example:
+    - 42
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Quantifying abundances of transcripts from RNA-Seq data, or more generally\
+  \ of target sequences using high-throughput sequencing reads.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test_data"
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "kallisto"
+- "quant"
+- "pseudoalignment"
+license: "BSD 2-Clause License"
+references:
+  doi:
+  - "10.1038/nbt.3519"
+links:
+  repository: "https://github.com/pachterlab/kallisto"
+  homepage: "https://pachterlab.github.io/kallisto/about"
+  documentation: "https://pachterlab.github.io/kallisto/manual"
+  issue_tracker: "https://github.com/pachterlab/kallisto/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: "ubuntu:22.04"
+  target_registry: "images.viash-hub.com"
+  target_tag: "bump_viash_0_9_4"
+  namespace_separator: "/"
+  setup:
+  - type: "docker"
+    run:
+    - "apt-get update && \\\napt-get install -y --no-install-recommends wget && \\\
+      \nwget --no-check-certificate https://github.com/pachterlab/kallisto/releases/download/v0.50.1/kallisto_linux-v0.50.1.tar.gz\
+      \ && \\\ntar -xzf kallisto_linux-v0.50.1.tar.gz && \\\nmv kallisto/kallisto\
+      \ /usr/local/bin/\n"
+  - type: "docker"
+    run:
+    - "echo \"kallisto: $(kallisto version | sed 's/kallisto, version //')\" > /var/software_versions.txt\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/kallisto/kallisto_quant/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/kallisto/kallisto_quant"
+  executable: "target/executable/kallisto/kallisto_quant/kallisto_quant"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/lofreq/lofreq_call/.config.vsh.yaml

@@ -0,0 +1,537 @@
+name: "lofreq_call"
+namespace: "lofreq"
+version: "bump_viash_0_9_4"
+authors:
+- name: "Kai Waldrant"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "kai@data-intuitive.com"
+      github: "KaiWaldrant"
+      orcid: "0009-0003-8555-1361"
+      linkedin: "kaiwaldrant"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Bioinformatician"
+    - name: "Open Problems"
+      href: "https://openproblems.bio"
+      role: "Contributor"
+argument_groups:
+- name: "Inputs"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "Input BAM file.\n"
+    info: null
+    example:
+    - "normal.bam"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--input_bai"
+    description: "Index file for the input BAM file.\n"
+    info: null
+    example:
+    - "normal.bai"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--ref"
+    alternatives:
+    - "-f"
+    description: "Indexed reference fasta file (gzip supported). Default: none.\n"
+    info: null
+    example:
+    - "reference.fasta"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--out"
+    alternatives:
+    - "-o"
+    description: "Vcf output file. Default: stdout.\n"
+    info: null
+    example:
+    - "output.vcf"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Arguments"
+  arguments:
+  - type: "string"
+    name: "--region"
+    alternatives:
+    - "-r"
+    description: "Limit calls to this region (chrom:start-end). Default: none.\n"
+    info: null
+    example:
+    - "chr1:1000-2000"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--bed"
+    alternatives:
+    - "-l"
+    description: "List of positions (chr pos) or regions (BED). Default: none.\n"
+    info: null
+    example:
+    - "regions.bed"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--min_bq"
+    alternatives:
+    - "-q"
+    description: "Skip any base with baseQ smaller than INT. Default: 6.\n"
+    info: null
+    example:
+    - 6
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--min_alt_bq"
+    alternatives:
+    - "-Q"
+    description: "Skip alternate bases with baseQ smaller than INT. Default: 6.\n"
+    info: null
+    example:
+    - 6
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--def_alt_bq"
+    alternatives:
+    - "-R"
+    description: "Overwrite baseQs of alternate bases (that passed bq filter) with\
+      \ this value (-1: use median ref-bq; 0: keep). Default: 0.\n"
+    info: null
+    example:
+    - 0
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--min_jq"
+    alternatives:
+    - "-j"
+    description: "Skip any base with joinedQ smaller than INT. Default: 0.\n"
+    info: null
+    example:
+    - 0
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--min_alt_jq"
+    alternatives:
+    - "-J"
+    description: "Skip alternate bases with joinedQ smaller than INT. Default: 0.\n"
+    info: null
+    example:
+    - 0
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--def_alt_jq"
+    alternatives:
+    - "-K"
+    description: "Overwrite joinedQs of alternate bases (that passed jq filter) with\
+      \ this value (-1: use median ref-bq; 0: keep). Default: 0.\n"
+    info: null
+    example:
+    - 0
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--no_baq"
+    alternatives:
+    - "-B"
+    description: "Disable use of base-alignment quality (BAQ).\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_idaq"
+    alternatives:
+    - "-A"
+    description: "Don't use IDAQ values (NOT recommended under ANY circumstances other\
+      \ than debugging).\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--del_baq"
+    alternatives:
+    - "-D"
+    description: "Delete pre-existing BAQ values, i.e. compute even if already present\
+      \ in BAM.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_ext_baq"
+    alternatives:
+    - "-e"
+    description: "Use 'normal' BAQ (samtools default) instead of extended BAQ (both\
+      \ computed on the fly if not already present in lb tag).\n"
+    info: null
+    direction: "input"
+  - type: "integer"
+    name: "--min_mq"
+    alternatives:
+    - "-m"
+    description: "Skip reads with mapping quality smaller than INT. Default: 0.\n"
+    info: null
+    example:
+    - 0
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--max_mq"
+    alternatives:
+    - "-M"
+    description: "Cap mapping quality at INT. Default: 255.\n"
+    info: null
+    example:
+    - 255
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--no_mq"
+    alternatives:
+    - "-N"
+    description: "Don't merge mapping quality in LoFreq's model.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--call_indels"
+    description: "Enable indel calls (note: preprocess your file to include indel\
+      \ alignment qualities!).\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--only_indels"
+    description: "Only call indels; no SNVs.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--src_qual"
+    alternatives:
+    - "-s"
+    description: "Enable computation of source quality.\n"
+    info: null
+    direction: "input"
+  - type: "file"
+    name: "--ign_vcf"
+    alternatives:
+    - "-S"
+    description: "Ignore variants in this vcf file for source quality computation.\
+      \ Multiple files can be given separated by commas.\n"
+    info: null
+    example:
+    - "variants.vcf"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--def_nm_q"
+    alternatives:
+    - "-T"
+    description: "If >= 0, then replace non-match base qualities with this default\
+      \ value. Default: -1.\n"
+    info: null
+    example:
+    - -1
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "double"
+    name: "--sig"
+    alternatives:
+    - "-a"
+    description: "P-Value cutoff / significance level. Default: 0.010000.\n"
+    info: null
+    example:
+    - 0.01
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--bonf"
+    alternatives:
+    - "-b"
+    description: "Bonferroni factor. 'dynamic' (increase per actually performed test)\
+      \ or INT. Default: Dynamic.\n"
+    info: null
+    example:
+    - "dynamic"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--min_cov"
+    alternatives:
+    - "-C"
+    description: "Test only positions having at least this coverage. Default: 1.\n\
+      (note: without --no-default-filter default filters (incl. coverage) kick in\
+      \ after predictions are done).\n"
+    info: null
+    example:
+    - 1
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--max_depth"
+    alternatives:
+    - "-d"
+    description: "Cap coverage at this depth. Default: 1000000.\n"
+    info: null
+    example:
+    - 1000000
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--illumina_13"
+    description: "Assume the quality is Illumina-1.3-1.7/ASCII+64 encoded.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--use_orphan"
+    description: "Count anomalous read pairs (i.e. where mate is not aligned properly).\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--plp_summary_only"
+    description: "No variant calling. Just output pileup summary per column.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_default_filter"
+    description: "Don't run default 'lofreq filter' automatically after calling variants.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--force_overwrite"
+    description: "Overwrite any existing output.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--verbose"
+    description: "Be verbose.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--debug"
+    description: "Enable debugging.\n"
+    info: null
+    direction: "input"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Call variants from a BAM file.\n\nLoFreq* (i.e. LoFreq version 2) is\
+  \ a fast and sensitive variant-caller for inferring SNVs and indels from next-generation\
+  \ sequencing data. It makes full use of base-call qualities and other sources of\
+  \ errors inherent in sequencing (e.g. mapping or base/indel alignment uncertainty),\
+  \ which are usually ignored by other methods or only used for filtering.\n\nLoFreq*\
+  \ can run on almost any type of aligned sequencing data (e.g. Illumina, IonTorrent\
+  \ or Pacbio) since no machine- or sequencing-technology dependent thresholds are\
+  \ used. It automatically adapts to changes in coverage and sequencing quality and\
+  \ can therefore be applied to a variety of data-sets e.g. viral/quasispecies, bacterial,\
+  \ metagenomics or somatic data.\n\nLoFreq* is very sensitive; most notably, it is\
+  \ able to predict variants below the average base-call quality (i.e. sequencing\
+  \ error rate). Each variant call is assigned a p-value which allows for rigorous\
+  \ false positive control. Even though it uses no approximations or heuristics, it\
+  \ is very efficient due to several runtime optimizations and also provides a (pseudo-)parallel\
+  \ implementation. LoFreq* is generic and fast enough to be applied to high-coverage\
+  \ data and large genomes. On a single processor it takes a minute to analyze Dengue\
+  \ genome sequencing data with nearly 4000X coverage, roughly one hour to call SNVs\
+  \ on a 600X coverage E.coli genome and also roughly an hour to run on a 100X coverage\
+  \ human exome dataset.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test_data"
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "variant calling"
+- "low frequancy variant calling"
+- "lofreq"
+- "lofreq/call"
+license: "MIT"
+references:
+  doi:
+  - "10.1093/nar/gks918"
+links:
+  repository: "https://github.com/viash-hub/biobox"
+  homepage: "https://csb5.github.io/lofreq/"
+  documentation: "https://csb5.github.io/lofreq/commands/"
+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/lofreq:2.1.5--py38h794fc9e_10"
+  target_registry: "images.viash-hub.com"
+  target_tag: "bump_viash_0_9_4"
+  namespace_separator: "/"
+  setup:
+  - type: "docker"
+    run:
+    - "version=$(lofreq version | grep 'version' | sed 's/version: //') && \\\necho\
+      \ \"lofreq: $version\" > /var/software_versions.txt\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/lofreq/call/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/lofreq/lofreq_call"
+  executable: "target/executable/lofreq/lofreq_call/lofreq_call"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml

@@ -0,0 +1,245 @@
+name: "lofreq_indelqual"
+namespace: "lofreq"
+version: "bump_viash_0_9_4"
+authors:
+- name: "Kai Waldrant"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "kai@data-intuitive.com"
+      github: "KaiWaldrant"
+      orcid: "0009-0003-8555-1361"
+      linkedin: "kaiwaldrant"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Bioinformatician"
+    - name: "Open Problems"
+      href: "https://openproblems.bio"
+      role: "Contributor"
+argument_groups:
+- name: "Inputs"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "Input BAM file.\n"
+    info: null
+    example:
+    - "normal.bam"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--ref"
+    alternatives:
+    - "-f"
+    description: "Reference sequence used for mapping (Only required for --dindel).\n"
+    info: null
+    example:
+    - "reference.fasta"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--out"
+    alternatives:
+    - "-o"
+    description: "Output BAM file.\n"
+    info: null
+    example:
+    - "output.bam"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Arguments"
+  arguments:
+  - type: "string"
+    name: "--uniform"
+    alternatives:
+    - "-u"
+    description: "Add this indel quality uniformly to all bases. Use two comma separated\
+      \ values to specify insertion and deletion quality separately. (clashes with\
+      \ --dindel).\n"
+    info: null
+    example:
+    - "50,50"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--dindel"
+    description: "Add Dindel's indel qualities (Illumina specific) (clashes with -u;\
+      \ needs --ref).\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--verbose"
+    description: "Be verbose.\n"
+    info: null
+    direction: "input"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Insert indel qualities into BAM file (required for indel predictions).\n\
+  \nThe preferred way of inserting indel qualities should be via GATK's BQSR (>=2)\
+  \ If that's not possible, use this subcommand.\nThe command has two modes: 'uniform'\
+  \ and 'dindel':\n- 'uniform' will assign a given value uniformly, whereas\n- 'dindel'\
+  \ will insert indel qualities based on Dindel (PMID 20980555).\nBoth will overwrite\
+  \ any existing values.\nDo not realign your BAM file afterwards!\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test_data"
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "bam"
+- "indel"
+- "qualities"
+- "indelqual"
+- "lofreq"
+- "lofreq/indelqual"
+license: "MIT"
+references:
+  doi:
+  - "10.1093/nar/gks918"
+links:
+  repository: "https://github.com/viash-hub/biobox"
+  homepage: "https://csb5.github.io/lofreq/"
+  documentation: "https://csb5.github.io/lofreq/commands/"
+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/lofreq:2.1.5--py38h794fc9e_10"
+  target_registry: "images.viash-hub.com"
+  target_tag: "bump_viash_0_9_4"
+  namespace_separator: "/"
+  setup:
+  - type: "docker"
+    run:
+    - "version=$(lofreq version | grep 'version' | sed 's/version: //') && \\\necho\
+      \ \"lofreq: $version\" > /var/software_versions.txt\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/lofreq/indelqual/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/lofreq/lofreq_indelqual"
+  executable: "target/executable/lofreq/lofreq_indelqual/lofreq_indelqual"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"

target/executable/multiqc/.config.vsh.yaml

@@ -0,0 +1,486 @@
+name: "multiqc"
+version: "bump_viash_0_9_4"
+authors:
+- name: "Dorien Roosen"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "dorien@data-intuitive.com"
+      github: "dorien-er"
+      linkedin: "dorien-roosen"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Scientist"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "File paths to be searched for analysis results to be included in\
+      \ the report.\n"
+    info: null
+    example:
+    - "data/results"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+- name: "Ouput"
+  arguments:
+  - type: "file"
+    name: "--output_report"
+    description: "Filepath of the generated report.\n"
+    info: null
+    example:
+    - "multiqc_report.html"
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_data"
+    description: "Output directory for parsed data files. If not provided, parsed\
+      \ data will not be published.\n"
+    info: null
+    example:
+    - "multiqc_data"
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_plots"
+    description: "Output directory for generated plots. If not provided, plots will\
+      \ not be published.\n"
+    info: null
+    example:
+    - "multiqc_plots"
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Modules and analyses to run"
+  arguments:
+  - type: "string"
+    name: "--include_modules"
+    description: "Use only these module"
+    info: null
+    example:
+    - "fastqc"
+    - "cutadapt"
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+  - type: "string"
+    name: "--exclude_modules"
+    description: "Do not use only these modules"
+    info: null
+    example:
+    - "fastqc"
+    - "cutadapt"
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+  - type: "string"
+    name: "--ignore_analysis"
+    info: null
+    example:
+    - "run_one/*"
+    - "run_two/*"
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+  - type: "string"
+    name: "--ignore_samples"
+    info: null
+    example:
+    - "sample_1*"
+    - "sample_3*"
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--ignore_symlinks"
+    description: "Ignore symlinked directories and files"
+    info: null
+    direction: "input"
+- name: "Sample name handling"
+  arguments:
+  - type: "boolean_true"
+    name: "--dirs"
+    description: "Prepend directory to sample names to avoid clashing filenames"
+    info: null
+    direction: "input"
+  - type: "integer"
+    name: "--dirs_depth"
+    description: "Prepend n directories to sample names. Negative number to take from\
+      \ start of path."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--full_names"
+    description: "Do not clean the sample names (leave as full file name)"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--fn_as_s_name"
+    description: "Use the log filename as the sample name"
+    info: null
+    direction: "input"
+  - type: "file"
+    name: "--replace_names"
+    description: "TSV file to rename sample names during report generation"
+    info: null
+    example:
+    - "replace_names.tsv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Report Customisation"
+  arguments:
+  - type: "string"
+    name: "--title"
+    description: "Report title. Printed as page header, used for filename if not otherwise\
+      \ specified.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--comment"
+    description: "Custom comment, will be printed at the top of the report.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--template"
+    description: "Report template to use.\n"
+    info: null
+    required: false
+    choices:
+    - "default"
+    - "gathered"
+    - "geo"
+    - "highcharts"
+    - "sections"
+    - "simple"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--sample_names"
+    description: "TSV file containing alternative sample names for renaming buttons\
+      \ in the report.\n"
+    info: null
+    example:
+    - "sample_names.tsv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--sample_filters"
+    description: "TSV file containing show/hide patterns for the report\n"
+    info: null
+    example:
+    - "sample_filters.tsv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--custom_css_file"
+    description: "Custom CSS file to add to the final report\n"
+    info: null
+    example:
+    - "custom_style_sheet.css"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--profile_runtime"
+    description: "Add analysis of how long MultiQC takes to run to the report\n"
+    info: null
+    direction: "input"
+- name: "MultiQC behaviour"
+  arguments:
+  - type: "boolean_true"
+    name: "--verbose"
+    description: "Increase output verbosity.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--quiet"
+    description: "Only show log warnings\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--strict"
+    description: "Don't catch exceptions, run additional code checks to help development.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--development"
+    description: "Development mode. Do not compress and minimise JS, export uncompressed\
+      \ plot data.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--require_logs"
+    description: "Require all explicitly requested modules to have log files. If not,\
+      \ MultiQC will exit with an error.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_megaqc_upload"
+    description: "Don't upload generated report to MegaQC, even if MegaQC options\
+      \ are found.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_ansi"
+    description: "Disable coloured log output.\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--cl_config"
+    description: "YAML formatted string that allows to customize MultiQC behaviour\
+      \ like input file detection.\n"
+    info: null
+    example:
+    - "qualimap_config: { general_stats_coverage: [20,40,200] }"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output format"
+  arguments:
+  - type: "boolean_true"
+    name: "--flat"
+    description: "Use only flat plots (static images).\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--interactive"
+    description: "Use only interactive plots (in-browser Javascript).\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--data_dir"
+    description: "Force the parsed data directory to be created.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_data_dir"
+    description: "Prevent the parsed data directory from being created.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--zip_data_dir"
+    description: "Compress the data directory.\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--data_format"
+    description: "Output parsed data in a different format than the default 'txt'.\n"
+    info: null
+    required: false
+    choices:
+    - "tsv"
+    - "csv"
+    - "json"
+    - "yaml"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--pdf"
+    description: "Creates PDF report with the 'simple' template. Requires Pandoc to\
+      \ be installed.\n"
+    info: null
+    direction: "input"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "MultiQC aggregates results from bioinformatics analyses across many\
+  \ samples into a single report.\nIt searches a given directory for analysis logs\
+  \ and compiles a HTML report. It's a general use tool, perfect for summarising the\
+  \ output from numerous bioinformatics tools.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test_data"
+info:
+  keywords:
+  - "QC"
+  - "html report"
+  - "aggregate analysis"
+  links:
+    homepage: "https://multiqc.info/"
+    documentation: "https://multiqc.info/docs/"
+    repository: "https://github.com/MultiQC/MultiQC"
+  references:
+    doi: "10.1093/bioinformatics/btw354"
+  licence: "GPL v3 or later"
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+license: "MIT"
+links:
+  repository: "https://github.com/viash-hub/biobox"
+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/multiqc:1.21--pyhdfd78af_0"
+  target_registry: "images.viash-hub.com"
+  target_tag: "bump_viash_0_9_4"
+  namespace_separator: "/"
+  setup:
+  - type: "docker"
+    run:
+    - "multiqc --version | sed 's/multiqc, version\\s\\(.*\\)/multiqc: \"\\1\"/' >\
+      \ /var/software_versions.txt\n"
+  test_setup:
+  - type: "apt"
+    packages:
+    - "jq"
+    interactive: false
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/multiqc/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/multiqc"
+  executable: "target/executable/multiqc/multiqc"
+  viash_version: "0.9.4"
+  git_commit: "be1cd83dd684d0a881a9c1f8e5b43d82a15d8b76"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-34-gbe1cd83"
+package_config:
+  name: "biobox"
+  version: "bump_viash_0_9_4"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'bump_viash_0_9_4'"
+  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"