name: cellranger_count_split
namespace: mapping
scope: "public"
description: Split 10x Cell Ranger output directory into separate output fields.
authors:
  - __merge__: /src/authors/angela_pisco.yaml
    roles: [ author ]
  - __merge__: /src/authors/samuel_d_souza.yaml
    roles: [ author ]
  - __merge__: /src/authors/robrecht_cannoodt.yaml
    roles: [ author, maintainer ]
arguments:
  - name: --input
    type: file
    required: true
    example: input_dir
    description: Output directory from a Cell Ranger count run.
  - name: --filtered_h5
    description: |
      Output path for the h5 file storing the filtered counts.
    type: file
    direction: output
    required: false
    example: filtered_feature_bc_matrix.h5
  - name: --metrics_summary
    description: |
      Where to store the 'metrics_summary' CSV file.
    type: file
    direction: output
    required: false
    example: metrics_summary.csv
  - name: --molecule_info
    description: |
      Where to store Cell Ranger's 'molecule_info.h5' file.
    type: file
    direction: output
    required: false
    example: molecule_info.h5
  - name: --bam
    description: |
      Location of output BAM files.
    type: file
    direction: output
    required: false
    example: possorted_genome_bam.bam
  - name: --bai
    description: |
      Where to store the BAM index files.
    type: file
    direction: output
    required: false
    example: possorted_genome_bam.bam.bai
  - name: --raw_h5
    description: |
      Output path for the h5 file storing the raw counts.
    type: file
    direction: output
    required: false
    # description: Counts in AnnData format.
    example: raw_feature_bc_matrix.h5
resources:
  - type: bash_script
    path: script.sh

engines:
- type: docker
  image: "ubuntu:jammy"
  setup:
    - type: docker
      run: apt update && apt upgrade -y

runners:
- type: executable
- type: nextflow