Build branch main with version main (781f668)

Build pipeline: viash-hub.craftbox.main-5sjkz

Source commit: 781f668839

Source message: FEAT: add untar (#3)

* FEAT: add untar

* Use meta_executable

target/executable/csv2fasta/.config.vsh.yaml

@@ -0,0 +1,248 @@
+name: "csv2fasta"
+version: "main"
+argument_groups:
+- name: "Inputs"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "CSV file to be processed."
+    info: null
+    example:
+    - "barcodes.csv"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--header"
+    description: "Parse the first line of the CSV file as a header.\n"
+    info: null
+    direction: "input"
+- name: "CSV dialect options"
+  description: "Options that can be used to override the automatically detected\n\
+    dialect of the CSV file.\n"
+  arguments:
+  - type: "string"
+    name: "--delimiter"
+    description: "Overwrite the column delimiter character.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--quote_character"
+    description: "Overwrite the character used to denote the start and end of a quoted\
+      \ item.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "CSV column arguments"
+  description: "Parameters for the selection of columns from the CSV file.\nOnly required\
+    \ when your CSV file contains more than 2 columns,\notherwise the first column\
+    \ will be used for the FASTA header\nand the second for the FASTA nucleotide sequences.\
+    \ This default\ncan still be overwritten by using the options below.\n"
+  arguments:
+  - type: "string"
+    name: "--sequence_column"
+    description: "Name of the column containing the sequences. Implies 'header'.\n\
+      Cannot be used together with 'sequence_column_index'.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--name_column"
+    description: "Name of the column describing the FASTA headers. Implies 'header'.\n\
+      Cannot be used together with 'name_column_index'.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--sequence_column_index"
+    description: "Index of the column to use as the FASTA sequences, counter from\
+      \ the left and\nstarting from 0. Cannot be used in combination with the 'sequence_column'\
+      \ argument.\n"
+    info: null
+    required: false
+    min: 0
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--name_column_index"
+    description: "Index of the column to use as the FASTA headers, counter from the\
+      \ left and\nstarting from 0. Cannot be used in combination with 'name_column'.\n"
+    info: null
+    required: false
+    min: 0
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    description: "Output fasta file."
+    info: null
+    example:
+    - "barcodes.fasta"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "python_script"
+  path: "script.py"
+  is_executable: true
+description: "Convert two columns from a CSV file to FASTA entries. The CSV file can\n\
+  contain an optional header and each row (other than the header) becomes\na single\
+  \ FASTA record. One of the two columns will be used as the names\nfor the FASTA\
+  \ entries, while the other become the sequences. The sequences\ncolumn must only\
+  \ contain characters that are valid IUPAC notation for \nnucleotides or a group\
+  \ thereof (wildcard characters).\n"
+test_resources:
+- type: "python_script"
+  path: "test_csv2fasta.py"
+  is_executable: true
+info: null
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+license: "MIT"
+links:
+  repository: "https://github.com/viash-hub/craftbox"
+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:slim"
+  target_registry: "images.viash-hub.com"
+  target_tag: "main"
+  namespace_separator: "/"
+  setup:
+  - type: "apt"
+    packages:
+    - "procps"
+    interactive: false
+  - type: "python"
+    user: false
+    packages:
+    - "dnaio"
+    upgrade: true
+  test_setup:
+  - type: "python"
+    user: false
+    packages:
+    - "pytest"
+    - "viashpy"
+    upgrade: true
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/csv2fasta/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/csv2fasta"
+  executable: "target/executable/csv2fasta/csv2fasta"
+  viash_version: "0.9.0-RC6"
+  git_commit: "781f66883977e37a849f228ee1dffddbb7acdf32"
+  git_remote: "https://github.com/viash-hub/craftbox"
+package_config:
+  name: "craftbox"
+  version: "main"
+  description: "A collection of custom-tailored scripts and applied tools.\n"
+  info: null
+  viash_version: "0.9.0-RC6"
+  source: "src"
+  target: "target"
+  config_mods:
+  - ".requirements.commands := ['ps']\n"
+  - ".engines += { type: \"native\" }"
+  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
+  - ".engines[.type == 'docker'].target_tag := 'main'"
+  keywords:
+  - "scripts"
+  - "custom"
+  - "implementations"
+  license: "MIT"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/viash-hub/craftbox"
+    issue_tracker: "https://github.com/viash-hub/craftbox/issues"