name: "process_samples"
namespace: "workflows/multiomics"
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: "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: "--rna_layer"
    description: "Input layer for the gene expression modality. If not specified,\
      \ .X is used."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--prot_layer"
    description: "Input layer for the antibody capture modality. If not specified,\
      \ .X is used."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--gdo_layer"
    description: "Input layer for the guide-derived oligonucleotide (GDO) data. If\
      \ not specified, .X is used."
    info: null
    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: ";"
- name: "Sample ID options"
  description: "Options for adding the id to .obs on the MuData object. Having a sample\
    \ \nid present in a requirement of several components for this pipeline.\n"
  arguments:
  - type: "boolean"
    name: "--add_id_to_obs"
    description: "Add the value passed with --id to .obs."
    info: null
    default:
    - true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--add_id_obs_output"
    description: ".Obs column to add the sample IDs to. Required and only used when\
      \ \n--add_id_to_obs is set to 'true'\n"
    info: null
    default:
    - "sample_id"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--add_id_make_observation_keys_unique"
    description: "Join the id to the .obs index (.obs_names). \nOnly used when --add_id_to_obs\
      \ is set to 'true'.\n"
    info: null
    default:
    - true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "RNA filtering options"
  arguments:
  - type: "integer"
    name: "--rna_min_counts"
    description: "Minimum number of counts captured per cell."
    info: null
    example:
    - 200
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--rna_max_counts"
    description: "Maximum number of counts captured per cell."
    info: null
    example:
    - 5000000
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--rna_min_genes_per_cell"
    description: "Minimum of non-zero values per cell."
    info: null
    example:
    - 200
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--rna_max_genes_per_cell"
    description: "Maximum of non-zero values per cell."
    info: null
    example:
    - 1500000
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--rna_min_cells_per_gene"
    description: "Minimum of non-zero values per gene."
    info: null
    example:
    - 3
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "double"
    name: "--rna_min_fraction_mito"
    description: "Minimum fraction of UMIs that are mitochondrial."
    info: null
    example:
    - 0.0
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "double"
    name: "--rna_max_fraction_mito"
    description: "Maximum fraction of UMIs that are mitochondrial."
    info: null
    example:
    - 0.2
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "double"
    name: "--rna_min_fraction_ribo"
    description: "Minimum fraction of UMIs that are mitochondrial."
    info: null
    example:
    - 0.0
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "double"
    name: "--rna_max_fraction_ribo"
    description: "Maximum fraction of UMIs that are mitochondrial."
    info: null
    example:
    - 0.2
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--skip_scrublet_doublet_detection"
    description: "Skip the scrublet doublet detection step."
    info: null
    direction: "input"
- name: "CITE-seq filtering options"
  arguments:
  - type: "integer"
    name: "--prot_min_counts"
    description: "Minimum number of counts per cell."
    info: null
    example:
    - 3
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--prot_max_counts"
    description: "Minimum number of counts per cell."
    info: null
    example:
    - 5000000
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--prot_min_proteins_per_cell"
    description: "Minimum of non-zero values per cell."
    info: null
    example:
    - 200
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--prot_max_proteins_per_cell"
    description: "Maximum of non-zero values per cell."
    info: null
    example:
    - 100000000
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--prot_min_cells_per_protein"
    description: "Minimum of non-zero values per protein."
    info: null
    example:
    - 3
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "GDO filtering options"
  arguments:
  - type: "integer"
    name: "--gdo_min_counts"
    description: "Minimum number of counts per cell."
    info: null
    example:
    - 3
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--gdo_max_counts"
    description: "Minimum number of counts per cell."
    info: null
    example:
    - 5000000
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--gdo_min_guides_per_cell"
    description: "Minimum of non-zero values per cell."
    info: null
    example:
    - 200
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--gdo_max_guides_per_cell"
    description: "Maximum of non-zero values per cell."
    info: null
    example:
    - 100000000
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--gdo_min_cells_per_guide"
    description: "Minimum of non-zero values per guide."
    info: null
    example:
    - 3
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Highly variable features detection"
  arguments:
  - type: "string"
    name: "--highly_variable_features_var_output"
    alternatives:
    - "--filter_with_hvg_var_output"
    description: "In which .var slot to store a boolean array corresponding to the\
      \ highly variable genes."
    info: null
    default:
    - "filter_with_hvg"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--highly_variable_features_obs_batch_key"
    alternatives:
    - "--filter_with_hvg_obs_batch_key"
    description: "If specified, highly-variable genes are selected within each batch\
      \ separately and merged. This simple \nprocess avoids the selection of batch-specific\
      \ genes and acts as a lightweight batch correction method.\n"
    info: null
    default:
    - "sample_id"
    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: "When specified, write the fraction of counts originating from mitochondrial\
      \ genes \n(based on --mitochondrial_gene_regex) to an .obs column with the specified\
      \ name.\nRequires --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 combined values specified for\n--var_name_mitochondrial_genes\
      \ and --highly_variable_features_var_output.\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: ","
- name: "PCA options"
  arguments:
  - type: "boolean_true"
    name: "--pca_overwrite"
    description: "Allow overwriting slots for PCA output."
    info: null
    direction: "input"
- name: "CLR options"
  arguments:
  - type: "integer"
    name: "--clr_axis"
    description: "Axis to perform the CLR transformation on."
    info: null
    default:
    - 0
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "RNA Scaling options"
  description: "Options for enabling scaling of the log-normalized data to unit variance\
    \ and zero mean.\nThe scaled data will be output a different layer and representation\
    \ with reduced dimensions\nwill be created and stored in addition to the non-scaled\
    \ data.\n"
  arguments:
  - type: "boolean_true"
    name: "--rna_enable_scaling"
    description: "Enable scaling for the RNA modality."
    info: null
    direction: "input"
  - type: "string"
    name: "--rna_scaling_output_layer"
    description: "Output layer where the scaled log-normalized data will be stored."
    info: null
    default:
    - "scaled"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--rna_scaling_pca_obsm_output"
    description: "Name of the .obsm key where the PCA representation of the log-normalized\n\
      and scaled data is stored.\n"
    info: null
    default:
    - "scaled_pca"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--rna_scaling_pca_loadings_varm_output"
    description: "Name of the .varm key where the PCA loadings of the log-normalized\
      \ and scaled\ndata is stored.\n"
    info: null
    default:
    - "scaled_pca_loadings"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--rna_scaling_pca_variance_uns_output"
    description: "Name of the .uns key where the variance and variance ratio will\
      \ be stored as a map.\nThe map will contain two keys: variance and variance_ratio\
      \ respectively.\n"
    info: null
    default:
    - "scaled_pca_variance"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--rna_scaling_umap_obsm_output"
    description: "Name of the .obsm key where the UMAP representation of the log-normalized\
      \ and scaled data is stored."
    info: null
    default:
    - "scaled_umap"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "double"
    name: "--rna_scaling_max_value"
    description: "Clip (truncate) data to this value after scaling. If not specified,\
      \ do not clip."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_false"
    name: "--rna_scaling_zero_center"
    description: "If set, omit zero-centering variables, which allows to handle sparse\
      \ input efficiently.\""
    info: null
    direction: "input"
resources:
- type: "nextflow_script"
  path: "main.nf"
  is_executable: true
  entrypoint: "run_wf"
- type: "file"
  path: "utils"
- type: "file"
  path: "nextflow_labels.config"
  dest: "nextflow_labels.config"
description: "A pipeline to analyse multiple multiomics samples."
test_resources:
- type: "nextflow_script"
  path: "test.nf"
  is_executable: true
  entrypoint: "test_wf"
- type: "nextflow_script"
  path: "test.nf"
  is_executable: true
  entrypoint: "test_wf2"
- type: "nextflow_script"
  path: "test.nf"
  is_executable: true
  entrypoint: "test_wf3"
- type: "nextflow_script"
  path: "test.nf"
  is_executable: true
  entrypoint: "test_wf4"
- type: "nextflow_script"
  path: "test.nf"
  is_executable: true
  entrypoint: "test_wf5"
- type: "file"
  path: "concat_test_data"
- type: "file"
  path: "pbmc_1k_protein_v3"
- type: "file"
  path: "10x_5k_lung_crispr"
info:
  test_dependencies:
  - name: "move_layer"
    namespace: "transform"
  - name: "remove_modality"
    namespace: "filter"
  - name: "assert_test_workflow_2_output"
    namespace: "test_workflows/multiomics/process_samples"
status: "enabled"
scope:
  image: "public"
  target: "public"
dependencies:
- name: "metadata/add_id"
  repository:
    type: "local"
- name: "workflows/multiomics/split_modalities"
  alias: "split_modalities_workflow"
  repository:
    type: "local"
- name: "dataflow/merge"
  repository:
    type: "local"
- name: "dataflow/concatenate_h5mu"
  repository:
    type: "local"
- name: "workflows/rna/rna_singlesample"
  repository:
    type: "local"
- name: "workflows/prot/prot_singlesample"
  repository:
    type: "local"
- name: "workflows/gdo/gdo_singlesample"
  repository:
    type: "local"
- name: "workflows/multiomics/process_batches"
  repository:
    type: "local"
license: "MIT"
links:
  repository: "https://github.com/openpipelines-bio/openpipeline"
  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/multiomics/process_samples/config.vsh.yaml"
  runner: "nextflow"
  engine: "native"
  output: "target/nextflow/workflows/multiomics/process_samples"
  executable: "target/nextflow/workflows/multiomics/process_samples/main.nf"
  viash_version: "0.9.4"
  git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62"
  git_remote: "https://github.com/openpipelines-bio/openpipeline"
  dependencies:
  - "target/nextflow/metadata/add_id"
  - "target/_private/nextflow/workflows/multiomics/split_modalities"
  - "target/nextflow/dataflow/merge"
  - "target/nextflow/dataflow/concatenate_h5mu"
  - "target/nextflow/workflows/rna/rna_singlesample"
  - "target/nextflow/workflows/prot/prot_singlesample"
  - "target/nextflow/workflows/gdo/gdo_singlesample"
  - "target/nextflow/workflows/multiomics/process_batches"
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"
