name: "pints_caller"
description: Main caller script for peak calling
keywords:
  - peak-calling
  - CoPRO
  - GRO-cap
  - PRO-cap
  - CAGE
  - NETCAGE
  - RAMPAGE
  - csRNA-seq
  - STRIPE-seq
  - PRO-seq
  - GRO-seq
tools:
  - "pints":
      description: "Peak Identifier for Nascent Transcripts Starts (PINTS)"
      homepage: "https://pints.yulab.org/"
      documentation: "https://github.com/hyulab/PINTS/blob/main/README.md"
      tool_dev_url: "https://github.com/hyulab/PINTS"
      doi: "https://doi.org/10.1038/s41587-022-01211-7"
      licence: "['GPL']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bams:
      type: file
      description: BAM/ file
      pattern: "*.{bam}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - divergent_TREs:
      type: file
      description: Divergent TREs
      pattern: "*_divergent_peaks.bed"
  - bidirectional_TREs:
      type: file
      description: Divergent TREs and convergent TREs
      pattern: "*_bidirectional_peaks.bed"
  - unidirectional_TREs:
      type: file
      description: Unidirectional TREs, maybe lncRNAs transcribed from enhancers (e-lncRNAs)
      pattern: "*_unidirectional_peaks.bed"

authors:
  - "@Emiller88"