name: "from_tiledb_to_h5mu"
namespace: "convert"
version: "v4.0.2"
authors:
- name: "Dries Schaumont"
  roles:
  - "author"
  - "maintainer"
  info:
    role: "Core Team Member"
    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 database"
  description: "Open a tileDB-SOMA database by URI."
  arguments:
  - type: "string"
    name: "--input_uri"
    description: "A URI pointing to a TileDB-SOMA database."
    info: null
    example:
    - "s3://bucket/path"
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--s3_region"
    description: "Region where the TileDB-SOMA database is hosted.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--endpoint"
    description: "Custom endpoint to use to connect to S3\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--s3_no_sign_request"
    description: "Do not sign S3 requests. Credentials will not be loaded if this\
      \ argument is provided.\n"
    info: null
    default:
    - false
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--input_modality"
    description: "TileDB-SOMA measurement to take the input from.\n"
    info: null
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--input_layers"
    description: "Layers to import from TileDB-SOMA database.\n"
    info: null
    required: true
    direction: "input"
    multiple: true
    multiple_sep: ";"
- name: "MuData output"
  arguments:
  - type: "file"
    name: "--output"
    description: "The output MuData file.\n"
    info: null
    example:
    - "output.h5mu"
    must_exist: true
    create_parent: true
    required: true
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--output_modality"
    description: "Name of the modality to write the results to.\n"
    info: null
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--output_compression"
    description: "Compression format to use for the output AnnData and/or Mudata objects.\n\
      By default no compression is applied.\n"
    info: null
    example:
    - "gzip"
    required: false
    choices:
    - "gzip"
    - "lzf"
    direction: "input"
    multiple: false
    multiple_sep: ";"
resources:
- type: "python_script"
  path: "script.py"
  is_executable: true
- type: "file"
  path: "setup_logger.py"
- type: "file"
  path: "nextflow_labels.config"
  dest: "nextflow_labels.config"
test_resources:
- type: "python_script"
  path: "test.py"
  is_executable: true
- type: "file"
  path: "tiledb"
info: null
status: "enabled"
scope:
  image: "public"
  target: "public"
license: "MIT"
links:
  repository: "https://github.com/openpipelines-bio/openpipeline"
  docker_registry: "ghcr.io"
runners:
- type: "executable"
  id: "executable"
  docker_setup_strategy: "ifneedbepullelsecachedbuild"
  docker_run_args:
  - "--env"
  - "AWS_ACCESS_KEY_ID"
  - "--env"
  - "AWS_SECRET_ACCESS_KEY"
- type: "nextflow"
  id: "nextflow"
  directives:
    label:
    - "highmem"
    - "midcpu"
    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"
    script:
    - "includeConfig(\"nextflow_labels.config\")"
  debug: false
  container: "docker"
engines:
- type: "docker"
  id: "docker"
  image: "python:3.12"
  target_registry: "images.viash-hub.com"
  target_tag: "v4.0.2"
  namespace_separator: "/"
  setup:
  - type: "python"
    user: false
    packages:
    - "anndata~=0.12.7"
    - "awkward"
    - "mudata~=0.3.2"
    - "tiledbsoma"
    script:
    - "exec(\"try:\\n  import zarr; from importlib.metadata import version\\nexcept\
      \ ModuleNotFoundError:\\n  exit(0)\\nelse:  assert int(version(\\\"zarr\\\"\
      ).partition(\\\".\\\")[0]) > 2\")"
    upgrade: true
  test_setup:
  - type: "apt"
    packages:
    - "git"
    interactive: false
  - type: "python"
    user: false
    packages:
    - "viashpy==0.8.0"
    github:
    - "openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils"
    upgrade: true
  - type: "python"
    user: false
    packages:
    - "moto[server]"
    - "boto3"
    upgrade: true
  entrypoint: []
  cmd: null
- type: "native"
  id: "native"
build_info:
  config: "src/convert/from_tiledb_to_h5mu/config.vsh.yaml"
  runner: "nextflow"
  engine: "docker|native"
  output: "target/nextflow/convert/from_tiledb_to_h5mu"
  executable: "target/nextflow/convert/from_tiledb_to_h5mu/main.nf"
  viash_version: "0.9.4"
  git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62"
  git_remote: "https://github.com/openpipelines-bio/openpipeline"
package_config:
  name: "openpipeline"
  version: "v4.0.2"
  summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
  description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
    \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
    \nIn terms of workflows, the following has been made available, but keep in mind\
    \ that\nindividual tools and functionality can be executed as standalone components\
    \ as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n\
    \  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample\
    \ processing: cell filtering and doublet detection.\n  * Multisample processing:\
    \ Count transformation, normalization, QC metric calulations.\n  * Integration:\
    \ Clustering, integration and batch correction using single and multimodal methods.\n\
    \  * Downstream analysis workflows\n"
  info:
    test_resources:
    - type: "s3"
      path: "s3://openpipelines-data"
      dest: "resources_test"
    nextflow_labels_ci:
    - path: "src/workflows/utils/labels_ci.config"
      description: "Adds the correct memory and CPU labels when running on the Viash\
        \ Hub CI."
  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
  - ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
    )'"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
  - ".engines[.type == 'docker'].target_tag := 'v4.0.2'"
  keywords:
  - "single-cell"
  - "multimodal"
  license: "MIT"
  organization: "vsh"
  links:
    repository: "https://github.com/openpipelines-bio/openpipeline"
    docker_registry: "ghcr.io"
    homepage: "https://openpipelines.bio"
    documentation: "https://openpipelines.bio/fundamentals"
    issue_tracker: "https://github.com/openpipelines-bio/openpipeline/issues"
