name: bedtools_genomecov
info: 
  migration_info:
    git_repo: https://github.com/nf-core/rnaseq.git
    paths: [modules/local/bedtools_genomecov.nf]
    last_sha: 0a1bdcfbb498987643b74e9fccab85ccd9f2a17d
description: Compute BEDGRAPH (-bg) summaries of feature coverage

argument_groups:
- name: "Input"
  arguments: 
  - name: "--strandedness"
    type: string
    choices: ["unstranded", "forward", "reverse", "auto"]
    description: Sample strand-specificity. 
  - name: "--bam"
    type: file
    description: Genome BAM file
  - name: "--extra_bedtools_args"
    type: string
    default: ''

- name: "Output"
  arguments: 
  - name: "--bedgraph_forward"
    type: file
    default: $id.forward.bedgraph
    direction: output
  - name: "--bedgraph_reverse"
    type: file
    default: $id.reverse.bedgraph
    direction: output

resources:
  - type: bash_script
    path: script.sh

test_resources:
  - type: bash_script
    path: test.sh
  - path: /testData/unit_test_resources/chr19.bam

engines:
  - type: docker
    image: ubuntu:22.04
    setup:
      - type: docker
        run: | 
          apt-get update && \
          apt-get install -y build-essential wget && \
          wget --no-check-certificate https://github.com/arq5x/bedtools2/releases/download/v2.31.0/bedtools.static && \
          mv bedtools.static /usr/local/bin/bedtools && \
          chmod a+x /usr/local/bin/bedtools
runners:
  - type: executable
  - type: nextflow
