name: fq_lint
namespace: fq
description: Validates a single or paired FASTQ file.
keywords: [fastq, lint, validate, quality-control]
links:
  homepage: https://github.com/stjude-rust-labs/fq/blob/master/README.md
  documentation: https://github.com/stjude-rust-labs/fq/blob/master/README.md
  repository: https://github.com/stjude-rust-labs/fq
license: MIT
requirements:
  commands: [fq]
authors:
  - __merge__: /src/_authors/robrecht_cannoodt.yaml
    roles: [ author, maintainer ]
  - __merge__: /src/_authors/emma_rousseau.yaml
    roles: [ author ]

argument_groups:
- name: "Input"
  description: "Input FASTQ files to validate."
  arguments:
  - name: "--input_1"
    type: file
    required: true
    description: "Read 1 source. Accepts both raw and gzipped FASTQ inputs."
    example: "reads_1.fastq.gz"
  - name: "--input_2"
    type: file
    required: false
    description: "Read 2 source. Accepts both raw and gzipped FASTQ inputs."
    example: "reads_2.fastq.gz"

- name: "Options"
  description: "Validation parameters."
  arguments:
  - name: "--lint_mode"
    type: string
    default: "panic"
    choices: ["panic", "log"]
    description: "Panic on first error or log all errors."
  - name: "--single_read_validation_level"
    type: string
    default: "high"
    choices: ["low", "medium", "high"]
    description: "Only use single read validators up to a given level."
  - name: "--paired_read_validation_level"
    type: string
    default: "high"
    choices: ["low", "medium", "high"]
    description: "Only use paired read validators up to a given level."
  - name: "--disable_validator"
    type: string
    multiple: true
    description: "Disable validators by code. Use multiple times to disable more than one."
  - name: "--record_definition_separator"
    type: string
    description: "Define a record definition separator."

resources:
  - type: bash_script
    path: script.sh

test_resources:
  - type: bash_script
    path: test.sh

engines:
  - type: docker
    image: quay.io/biocontainers/fq:0.12.0--h9ee0642_0
    setup:
      - type: docker
        run: |
          fq -V | sed 's#fq \([0-9.]*\) .*#fq: \1#' > /var/software_versions.txt

runners:
  - type: executable
  - type: nextflow
