name: htrnaseq
namespace: workflows
argument_groups:
  - name: Input arguments
    arguments:
      - name: --input_r1
        description: |
          Forward reads in FASTQ format. Multiple files can be provided which will
          be demultiplexed separately before joining the results for each individual well.
        type: file
        required: true
        multiple: true
      - name: --input_r2
        description: |
          Reverse reads in FASTQ format. Multiple files can be provided which will
          be demultiplexed separately before joining the results for each individual well.
        type: file
        required: true
        multiple: true
      - name: --barcodesFasta
        type: file
        required: true
      - name: --genomeDir
        type: file
        required: true
      - name: --annotation
        type: file
        required: true
  - name: Output arguments
    arguments:
      - name: --fastq_output_r1
        description: List of demultiplexed fastq files
        type: file
        direction: output
        multiple: true
        required: true
        default: "fastq/*_R1_001.fastq"
      - name: --fastq_output_r2
        description: List of demultiplexed fastq files
        type: file
        direction: output
        multiple: true
        required: true
        default: "fastq/*_R2_001.fastq"
      - name: --star_output
        description: Output from mapping with STAR
        type: file
        direction: output
        multiple: true
        required: true
        default: $id/star/*
      - name: "--nrReadsNrGenesPerChrom"
        type: file
        direction: output
        required: true
        default: "nrReadsNrGenesPerChrom.$id.txt"
      - name: "--star_qc_metrics"
        type: file
        direction: output
        required: true
        default: "starLogs.$id.txt"
      - name: "--eset"
        type: file
        direction: output
        required: true
        default: eset.$id.rds
      - name: "--f_data"
        type: file
        direction: output
        required: true
        default: fData.$id.tsv
      - name: "--p_data"
        type: file
        direction: output
        required: true
        default: pData.$id.tsv
resources:
  - type: nextflow_script
    path: main.nf
    entrypoint: run_wf
test_resources:
  - type: nextflow_script
    path: test.nf
    entrypoint: test_wf
dependencies:
  - name: stats/combine_star_logs
    repository: local
  - name: stats/generate_pool_statistics
    repository: local
  - name: stats/generate_well_statistics
    repository: local
  - name: workflows/well_demultiplex
    repository: local
  - name: workflows/parallel_map_wf
    repository: local
  - name: workflows/utils/groupWells
    repository: local
  - name: eset/create_eset
    repository: local
  - name: eset/create_fdata
    repository: local
  - name: eset/create_pdata
    repository: local
repositories:
  - name: local
    type: local
  - name: bb
    type: vsh
    repo: biobox
    tag: v0.1.0

runners:
  - type: nextflow

engines:
  - type: native
