name: "fastqc"
namespace: "qc"
scope: "public"
description: |
  Fastqc component, please see https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. This component can take one or more files (by means of shell globbing) or a complete directory.
arguments:
  - name: "--mode"
    alternatives: [ "-m" ]
    type: string
    choices: [ files, dir ]
    default: files
    description: The mode in which the component works. Can be either files or dir.
  - name: "--input"
    alternatives: [ "-i" ]
    type: file
    required: true
    description: Directory containing input fastq files.
    example: fastq_dir/
  - name: "--output"
    alternatives: [ "-o" ]
    type: file
    direction: output
    required: true
    description: Output directory to write reports to.
    example: qc/
  - name: "--threads"
    alternatives: ["-t"]
    type: integer
    required: false
    description: |
      Specifies the number of files which can be processed simultaneously. Each thread will be allocated 250MB of
      memory.
resources:
  - type: bash_script
    path: script.sh
test_resources:
  - type: bash_script
    path: test.sh
  - path: /resources_test/cellranger_tiny_fastq/cellranger_tiny_fastq

engines:
- type: docker
  image: ubuntu:24.04
  setup:
    - type: apt
      packages: [ fastqc ]

runners:
- type: executable
- type: nextflow
  directives:
    label: [lowcpu, midmem]
