name: combine_samples
namespace: dataflow
description: Combine fastq files from across samples into one event with a list of fastq files per orientation.
argument_groups:
  - name: Input arguments
    arguments:
      - name: "--id"
        description: "ID of the new event"
        type: string
        required: true
      - name: --forward_input
        type: file
        required: true
        multiple: true
      - name: --reverse_input
        type: file
        required: false
        multiple: true
      - name: "--falco_dir"
        type: file
        required: true
  - name: Output arguments
    arguments:
      - name: --output_forward
        type: file
        direction: output
        multiple: true
        required: true
      - name: --output_reverse
        type: file
        direction: output
        multiple: true
        required: false
      - name: "--output_falco"
        type: file
        direction: output
        required: true
        multiple: true
resources:
  - type: nextflow_script
    path: main.nf
    entrypoint: run_wf

runners:
  - type: nextflow

engines:
  - type: native