name: generate_pool_statistics
namespace: "stats"
authors:
  - __merge__: /src/base/authors/dries_schaumont.yaml
    roles: [ author, maintainer ]
  - __merge__: /src/base/authors/marijke_van_moerbeke.yaml
    roles: [ contributor ]
argument_groups:
  - name: "Arguments"
    arguments:
      - name: "--nrReadsNrGenesPerChrom"
        type: file
        multiple: true
        description: |
          Path to an output file that contains a .tsv formatted table describing
          per chromosome the number of reads that were mapped to that chromosome (NumberOfReads
          column) and the number of genes on that chromosome that had at least one
          read mapped to it (NumberOfGenes).
        direction: input
        default: [processedBamFile_well1.tsv, processedBamfile_well2.tsv]
      - name: "--nrReadsNrGenesPerChromPool"
        direction: output
        type: file
        multiple: false
        description: |
          Pivot table in tsv format of the combined input nrReadsNrGenesPerChrom files. Describes
          per chromosome (as columns) the number of reads, as well as the total number 
          of reads per cell barcode and the percentage of nuclear, ERCC and mitochondrial
          reads.
        example: "nrReadsNrGenesPerChrom.txt"

resources:
- type: python_script
  path: script.py

test_resources:
  - type: python_script
    path: test.py

engines:
  - type: docker
    image: python:3.12-slim
    setup:
      - type: apt
        packages:
          - procps
      - type: python
        packages:
          - pandas
    test_setup:
      - type: python
        packages:
          - viashpy
runners:
  - type: executable
  - type: nextflow