name: concatRuns
namespace: utils
description: |
  Concatenate well FASTQ files from different runs in order to increase sequencing depth.
arguments:
  - name: "--input_r1"
    type: file
    required: true
    multiple: true
  - name: "--input_r2"
    type: file
    required: true
    multiple: true
  - name: "--sample_id"
    type: string
    required: true
  - name: "--output_r1"
    type: file
    multiple: true
    description: Path to read 1 fastq/fasta file
    direction: output
  - name: "--output_r2"
    type: file
    multiple: true
    description: Path to read 2 fastq/fasta file
    direction: output
resources:
  - type: nextflow_script
    path: main.nf
    entrypoint: run_wf
dependencies:
    - name: concat_text
      repository: cb
repositories:
  - name: cb
    type: vsh
    repo: craftbox
    tag: v0.3.1
runners:
  - type: nextflow

engines:
  - type: native
