name: "rseqc_junctionannotation"
namespace: "rseqc"
info:
  migration_info:
    git_repo: https://github.com/nf-core/rnaseq.git
    paths: [modules/nf-core/rseqc/junctionannotation/main.nf]
    last_sha: 
description: |
  Compare detected splice junctions to reference gene model.

argument_groups:
- name: "Input"
  arguments: 
  - name: "--input"
    type: file 
    required: true
    description: input alignment file in BAM or SAM format

  - name: "--refgene"
    type: file 
    required: true
    description: Reference gene model in bed format

  - name: "--map_qual"
    type: integer
    required: false
    default: 30 
    description: Minimum mapping quality (phred scaled) to determine uniquely mapped reads, default=30.
    min: 0

  - name: "--min_intron"
    type: integer
    required: false
    default: 50
    min: 1 
    description: Minimum intron length (bp), default = 50.
    
- name: "Output"
  arguments: 
  - name: "--output_log"
    type: file
    direction: output
    required: false
    default: $id.junction_annotation.log
    description: output log of junction annotation script

  - name: "--output_plot_r"
    type: file
    direction: output
    required: false
    default: $id.junction_annotation_plot.r
    description: r script to generate splice_junction and splice_events plot

  - name: "--output_junction_bed"
    type: file
    direction: output
    required: false
    default: $id.junction_annotation.bed
    description: junction annotation file (bed format)

  - name: "--output_junction_interact"
    type: file
    direction: output
    required: false
    default: $id.junction_annotation.Interact.bed
    description: interact file (bed format) of junctions. Can be uploaded to UCSC genome browser or converted to bigInteract (using bedToBigBed program) for visualization.

  - name: "--output_junction_sheet"
    type: file
    direction: output
    required: false
    default: $id.junction_annotation.xls
    description: junction annotation file (xls format)

  - name: "--output_splice_events_plot"
    type: file
    direction: output
    required: false
    default: $id.splice_events.pdf
    description: plot of splice events (pdf)

  - name: "--output_splice_junctions_plot"
    type: file
    direction: output
    required: false
    default: $id.splice_junctions_plot.pdf
    description: plot of junctions (pdf)

resources:
  - type: bash_script
    path: script.sh
test_resources:
  - type: bash_script
    path: test.sh
  - path: /testData/unit_test_resources/sarscov2/test.paired_end.sorted.bam
  - path: /testData/unit_test_resources/sarscov2/test.bed12
  
engines:
- type: docker
  image: ubuntu:22.04
  setup:   
    - type: apt
      packages: [ python3-pip, r-base]
    - type: python
      packages: [ RSeQC ]
runners: 
- type: executable
- type: nextflow