name: "fastqc"
info:
  migration_info:
    git_repo: https://github.com/nf-core/rnaseq.git
    paths: [modules/nf-core/fastqc/main.nf, modules/nf-core/fastqc/meta.yml]
    last_sha: 54721c6946daf6d602d7069dc127deef9cbe6b33
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.

argument_groups:
- name: "Input"
  arguments: 
  - name: "--paired"
    type: boolean 
    required: false
    default: false
    description: Paired fastq files or not?
  - name: "--input"
    type: file
    required: true
    multiple: true
    multiple_sep: ","
    description: Input fastq files, either one or two (paired)
    example: sample.fastq
    
- name: "Output"
  arguments:   
  - name: "--fastqc_html_1"
    type: file
    direction: output
    description: FastQC HTML report for read 1.
    default: $id.read_1.fastqc.html
  - name: "--fastqc_html_2"
    type: file
    direction: output
    description: FastQC HTML report for read 2.
    required: false
    must_exist: false
    default: $id.read_2.fastqc.html
  - name: "--fastqc_zip_1"
    type: file
    direction: output
    description: FastQC report archive for read 1.
    default: $id.read_1.fastqc.zip
  - name: "--fastqc_zip_2"
    type: file
    direction: output
    description: FastQC report archive for read 2.
    required: false
    must_exist: false
    default: $id.read_2.fastqc.zip

resources:
  - type: bash_script
    path: script.sh

test_resources:
  - type: bash_script
    path: test.sh
  - path: /testData/minimal_test/input_fastq/SRR6357070_1.fastq.gz
  - path: /testData/minimal_test/input_fastq/SRR6357070_2.fastq.gz

engines:
  - type: docker
    image: ubuntu:22.04
    setup:
      - type: apt
        packages: [ fastqc ]
runners:
  - type: executable
  - type: nextflow
