name: runner
namespace: workflows
description: Runner for HT RNA-seq pipeline
argument_groups:
  - name: Input arguments
    arguments:
      - name: --input
        description: Base directory of the form `s3:/<bucket>/Sequencing/<Sequencer>/<RunID>/<demultiplex_dir>`
        type: file
        required: true
      - name: --barcodesFasta
        type: file
        required: true
      - name: --genomeDir
        type: file
        required: true
      - name: --annotation
        type: file
        required: true
      - name: --ignore
        description: "Pool names to ignore."
        type: string
        multiple: true
        default: ["Undetermined"]
      - name: "--umi_length"
        description: |
          Length of the UMI sequences
        type: integer
        min: 1
        default: 10
      - name: "--run_params"
        type: file
        required: false
        direction: output
        default: params.yaml
  - name: Metadata arguments
    arguments:
      - name: --id
        description: Unique identifier for the run
        type: string
      - name: --project_id
        description: Project ID
        type: string
        required: true
      - name: --experiment_id
        description: Experiment ID
        type: string
        required: true
  - name: Publish arguments
    arguments:
      - name: --fastq_publish_dir
        type: string
        required: true
      - name: --results_publish_dir
        type: string
        required: true

resources:
  - type: nextflow_script
    path: main.nf
    entrypoint: run_wf

test_resources:
  - type: nextflow_script
    path: test.nf
    entrypoint: test_wf

dependencies:
  - name: utils/listInputDir
    repository: local
  - name: workflows/htrnaseq
    repository: local
  - name: io/publish_fastqs
    repository: local
  - name: io/publish_results
    repository: local
  - name: utils/save_params
    repository: local

runners:
  - type: nextflow

engines:
  - type: native
