name: "generate_pool_statistics"
namespace: "stats"
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"
- name: "Marijke Van Moerbeke"
  roles:
  - "contributor"
  info:
    links:
      github: "mvanmoerbeke"
      orcid: "0000-0002-3097-5621"
      linkedin: "marijke-van-moerbeke-84303a34"
    organizations:
    - name: "OpenAnalytics"
      href: "https://www.openanalytics.eu"
      role: "Statistical Consultant"
argument_groups:
- name: "Arguments"
  arguments:
  - type: "file"
    name: "--nrReadsNrGenesPerChrom"
    description: "Path to an output file that contains a .tsv formatted table describing\n\
      per chromosome the number of reads that were mapped to that chromosome (NumberOfReads\n\
      column) and the number of genes on that chromosome that had at least one\nread\
      \ mapped to it (NumberOfGenes).\n"
    info: null
    default:
    - "processedBamFile_well1.tsv"
    - "processedBamfile_well2.tsv"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "file"
    name: "--nrReadsNrGenesPerChromPool"
    description: "Pivot table in tsv format of the combined input nrReadsNrGenesPerChrom\
      \ files. Describes\nper chromosome (as columns) the number of reads, as well\
      \ as the total number \nof reads per cell barcode and the percentage of nuclear,\
      \ ERCC and mitochondrial\nreads.\n"
    info: null
    example:
    - "nrReadsNrGenesPerChrom.txt"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
resources:
- type: "python_script"
  path: "script.py"
  is_executable: true
- type: "file"
  path: "nextflow_labels.config"
  dest: "nextflow_labels.config"
test_resources:
- type: "python_script"
  path: "test.py"
  is_executable: true
info: null
status: "enabled"
requirements:
  commands:
  - "ps"
license: "MIT"
links:
  repository: "https://github.com/viash-hub/htrnaseq"
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"
    script:
    - "includeConfig(\"nextflow_labels.config\")"
  debug: false
  container: "docker"
engines:
- type: "docker"
  id: "docker"
  image: "python:3.12-slim"
  target_registry: "images.viash-hub.com"
  target_tag: "main"
  namespace_separator: "/"
  setup:
  - type: "apt"
    packages:
    - "procps"
    interactive: false
  - type: "python"
    user: false
    packages:
    - "pandas"
    upgrade: true
  test_setup:
  - type: "python"
    user: false
    packages:
    - "viashpy"
    upgrade: true
  entrypoint: []
  cmd: null
- type: "native"
  id: "native"
build_info:
  config: "src/stats/generate_pool_statistics/config.vsh.yaml"
  runner: "executable"
  engine: "docker|native"
  output: "target/executable/stats/generate_pool_statistics"
  executable: "target/executable/stats/generate_pool_statistics/generate_pool_statistics"
  viash_version: "0.9.0"
  git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3"
  git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
  name: "htrnaseq"
  version: "main"
  description: "High-throughput pipeline [WIP]\n"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/htrnaseq/v1/"
      dest: "resources_test"
  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
    \ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
    \ dest: 'nextflow_labels.config'}\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
  - ".engines[.type == 'docker'].target_tag := 'main'"
  keywords:
  - "bioinformatics"
  - "sequence"
  - "high-throughput"
  - "mapping"
  - "counting"
  - "pipeline"
  license: "MIT"
  organization: "vsh"
  links:
    repository: "https://github.com/viash-hub/htrnaseq"
    issue_tracker: "https://github.com/viash-hub/htrnaseq/issues"