Build branch main with version main (a13b57d)

Build pipeline: viash-hub.biobox.main-t7scl

Source commit: a13b57d04a

Source message: Add bases2fastq (#167)

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

@@ -0,0 +1,421 @@
+name: "bases2fastq"
+version: "main"
+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"
+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: "main"
+  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: "0.9.0"
+  git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
+  git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-26-ga13b57d"
+package_config:
+  name: "biobox"
+  version: "main"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.0"
+  source: "src"
+  target: "target"
+  config_mods:
+  - ".requirements.commands := ['ps']\n"
+  - ".engines += { type: \"native\" }"
+  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
+  - ".engines[.type == 'docker'].target_tag := 'main'"
+  keywords:
+  - "bioinformatics"
+  - "modules"
+  - "sequencing"
+  license: "MIT"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/viash-hub/biobox"
+    issue_tracker: "https://github.com/viash-hub/biobox/issues"