name: "spatial_qc"
namespace: "workflows/qc"
version: "build_main"
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"
- name: "Dorien Roosen"
  roles:
  - "contributor"
  info:
    role: "Core Team Member"
    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"
- name: "Weiwei Schultz"
  roles:
  - "contributor"
  info:
    role: "Contributor"
    organizations:
    - name: "Janssen R&D US"
      role: "Associate Director Data Sciences"
argument_groups:
- name: "Inputs"
  arguments:
  - type: "string"
    name: "--id"
    description: "ID of the sample."
    info: null
    example:
    - "foo"
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--input"
    alternatives:
    - "-i"
    description: "Path to the sample."
    info: null
    example:
    - "input.h5mu"
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--modality"
    description: "Which modality to process."
    info: null
    default:
    - "rna"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--layer"
    description: "Use specified layer for calculation of qc metrics. If not specified,\
      \ adata.X is used."
    info: null
    example:
    - "raw_counts"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Mitochondrial & Ribosomal Gene Detection"
  arguments:
  - type: "string"
    name: "--var_gene_names"
    description: ".var column name to be used to detect mitochondrial/ribosomal genes\
      \ instead of .var_names (default if not set).\nGene names matching with the\
      \ regex value from --mitochondrial_gene_regex or --ribosomal_gene_regex will\
      \ be \nidentified as mitochondrial or ribosomal genes, respectively.\n"
    info: null
    example:
    - "gene_symbol"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--var_name_mitochondrial_genes"
    description: "In which .var slot to store a boolean array corresponding the mitochondrial\
      \ genes.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--obs_name_mitochondrial_fraction"
    description: ".Obs slot to store the fraction of reads found to be mitochondrial.\
      \ Defaults to 'fraction_' suffixed by the value of --var_name_mitochondrial_genes\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--mitochondrial_gene_regex"
    description: "Regex string that identifies mitochondrial genes from --var_gene_names.\n\
      By default will detect human and mouse mitochondrial genes from a gene symbol.\n"
    info: null
    default:
    - "^[mM][tT]-"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--var_name_ribosomal_genes"
    description: "In which .var slot to store a boolean array corresponding the ribosomal\
      \ genes.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--obs_name_ribosomal_fraction"
    description: "When specified, write the fraction of counts originating from ribosomal\
      \ genes \n(based on --ribosomal_gene_regex) to an .obs column with the specified\
      \ name.\nRequires --var_name_ribosomal_genes.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--ribosomal_gene_regex"
    description: "Regex string that identifies ribosomal genes from --var_gene_names.\n\
      By default will detect human and mouse ribosomal genes from a gene symbol.\n"
    info: null
    default:
    - "^[Mm]?[Rr][Pp][LlSs]"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "QC metrics calculation options"
  arguments:
  - type: "string"
    name: "--var_qc_metrics"
    description: "Keys to select a boolean (containing only True or False) column\
      \ from .var.\nFor each cell, calculate the proportion of total values for genes\
      \ which are labeled 'True', \ncompared to the total sum of the values for all\
      \ genes. Defaults to the value from\n--var_name_mitochondrial_genes.\n"
    info: null
    example:
    - "ercc,highly_variable"
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ","
  - type: "integer"
    name: "--top_n_vars"
    description: "Number of top vars to be used to calculate cumulative proportions.\n\
      If not specified, proportions are not calculated. `--top_n_vars 20,50` finds\n\
      cumulative proportion to the 20th and 50th most expressed vars.\n"
    info: null
    default:
    - 50
    - 100
    - 200
    - 500
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ","
  - type: "string"
    name: "--output_obs_num_nonzero_vars"
    description: "Name of column in .obs describing, for each observation, the number\
      \ of stored values\n(including explicit zeroes). In other words, the name of\
      \ the column that counts\nfor each row the number of columns that contain data.\n"
    info: null
    default:
    - "num_nonzero_vars"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--output_obs_total_counts_vars"
    description: "Name of the column for .obs describing, for each observation (row),\n\
      the sum of the stored values in the columns.\n"
    info: null
    default:
    - "total_counts"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--output_var_num_nonzero_obs"
    description: "Name of column describing, for each feature, the number of stored\
      \ values\n(including explicit zeroes). In other words, the name of the column\
      \ that counts\nfor each column the number of rows that contain data.\n"
    info: null
    default:
    - "num_nonzero_obs"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--output_var_total_counts_obs"
    description: "Name of the column in .var describing, for each feature (column),\n\
      the sum of the stored values in the rows.\n"
    info: null
    default:
    - "total_counts"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--output_var_obs_mean"
    description: "Name of the column in .obs providing the mean of the values in each\
      \ row.\n"
    info: null
    default:
    - "obs_mean"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--output_var_pct_dropout"
    description: "Name of the column in .obs providing for each feature the percentage\
      \ of\nobservations the feature does not appear on (i.e. is missing). Same as\
      \ `--output_var_num_nonzero_obs`\nbut percentage based.\n"
    info: null
    default:
    - "pct_dropout"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Outputs"
  arguments:
  - type: "file"
    name: "--output"
    description: "Destination path to the output."
    info: null
    example:
    - "output.h5mu"
    must_exist: true
    create_parent: true
    required: true
    direction: "output"
    multiple: false
    multiple_sep: ";"
resources:
- type: "nextflow_script"
  path: "main.nf"
  is_executable: true
  entrypoint: "run_wf"
- type: "file"
  path: "nextflow_labels.config"
  dest: "nextflow_labels.config"
description: "A pipeline to add basic qc statistics to a MuData containing spatial\
  \ data."
test_resources:
- type: "nextflow_script"
  path: "test.nf"
  is_executable: true
  entrypoint: "test_wf"
- type: "file"
  path: "xenium_tiny.h5mu"
info:
  test_dependencies:
  - name: "qc_test"
    namespace: "test_workflows/qc"
status: "enabled"
scope:
  image: "public"
  target: "public"
dependencies:
- name: "workflows/qc/qc"
  alias: "spatial_qc_workflow"
  repository:
    type: "github"
    repo: "openpipelines-bio/openpipeline"
    tag: "2.1.2"
repositories:
- type: "github"
  name: "openpipeline"
  repo: "openpipelines-bio/openpipeline"
  tag: "2.1.2"
links:
  repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
  docker_registry: "ghcr.io"
runners:
- 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: "native"
  id: "native"
build_info:
  config: "src/workflows/qc/spatial_qc/config.vsh.yaml"
  runner: "nextflow"
  engine: "native"
  output: "target/nextflow/workflows/qc/spatial_qc"
  executable: "target/nextflow/workflows/qc/spatial_qc/main.nf"
  viash_version: "0.9.4"
  git_commit: "6f308e6a3cca52f1283fbba734a3cdc858e18e1b"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
  dependencies:
  - "target/dependencies/github/openpipelines-bio/openpipeline/2.1.2/nextflow/workflows/qc/qc"
package_config:
  name: "openpipeline_spatial"
  version: "build_main"
  info:
    test_resources:
    - type: "s3"
      path: "s3://openpipelines-bio/openpipeline_spatial/resources_test"
      dest: "resources_test"
  repositories:
  - type: "github"
    name: "openpipeline"
    repo: "openpipelines-bio/openpipeline"
    tag: "2.1.2"
  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 := 'build_main'"
  organization: "vsh"
  links:
    repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
    docker_registry: "ghcr.io"