name: seqtk_sample
namespace: seqtk
description: Subsamples sequences from FASTA/Q files.
keywords: [sample, FASTA, FASTQ]
links:
  repository: https://github.com/lh3/seqtk/tree/v1.4
license: MIT
authors:
  - __merge__: /src/_authors/jakub_majercik.yaml
    roles: [ author, maintainer ]

argument_groups:
  - name: Inputs
    arguments:
      - name: --input
        type: file
        description: The input FASTA/Q file.
        required: true

  - name: Outputs
    arguments:
      - name: --output
        type: file
        description: The output FASTA/Q file.
        required: true
        direction: output

  - name: Options
    arguments:
      - name: --seed
        type: integer
        description: Seed for random generator.
        example: 42
      - name: --fraction_number
        type: double
        description: Fraction or number of sequences to sample.
        required: true
        example: 0.1
      - name: --two_pass_mode
        type: boolean_true
        description: Twice as slow but with much reduced memory

resources:
  - type: bash_script
    path: script.sh
test_resources:
  - type: bash_script
    path: test.sh
  - type: file
    path: ../test_data

engines:
  - type: docker
    image: quay.io/biocontainers/seqtk:1.4--he4a0461_2
runners:
  - type: executable
  - type: nextflow