name: "multiqc"
namespace: "qc"
scope: "public"
description: |
  MultiQC aggregates results from bioinformatics analyses across many samples into a single report.
  It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.
arguments:
  - name: "--input"
    alternatives: [ "-i" ]
    type: file
    required: true
    multiple: true
    description: Inputs for MultiQC.
    example: input.txt
  - name: "--output"
    alternatives: [ "-o" ]
    type: file
    direction: output
    required: true
    description: Create report in the specified output directory.
    example: path/to/report/
resources:
  - type: python_script
    path: script.py
test_resources:
  - type: python_script
    path: test.py
  - path: /resources_test/10x_5k_anticmv/fastqc/

engines:
- type: docker
  image: python:3.13-slim
  setup:
    - type: apt
      packages: 
        - procps
    - type: python
      packages: [ multiqc ]
  test_setup:
    - type: python
      __merge__: [ /src/base/requirements/viashpy.yaml, .]

runners:
- type: executable
- type: nextflow
  directives:
    label: [singlecpu, lowmem]
