name: stringtie
info:
  migration_info:
    git_repo: https://github.com/nf-core/rnaseq.git
    paths: [modules/nf-core/stringtie/stringtie/main.nf, modules/nf-core/stringtie/stringtie/meta.yml]
    last_sha: 55398de6ab7577acfe9b1180016a93d7af7eb859
description: | 
  Transcript assembly and quantification for RNA-Seq

argument_groups:
- name: "Input"
  arguments: 
  - name: "--strandedness"
    type: string
    description: Forward or reverse strand?
  - name: "--bam"
    type: file
  - name: "--annotation_gtf"
    type: file
  - name: "--extra_stringtie_args"
    type: string
    description: Extra arguments for running StringTie
  - name: "--stringtie_ignore_gtf"
    type: boolean
    description: Perform reference-guided de novo assembly of transcripts using StringTie, i.e. don't restrict to those in GTF file.
    
- name: "Output"
  arguments: 
  - name: "--transcript_gtf"
    type: file
    default: $id.$key.transcripts.gtf
    direction: output
  - name: "--coverage_gtf"
    type: file
    default: $id.$key.coverage.gtf
    direction: output
  - name: "--abundance"
    type: file
    default: $id.$key.abundance.txt
    direction: output
  - name: "--ballgown"
    type: file
    description: for running ballgown
    default: $id.$key.ballgown
    direction: output

resources: 
  - type: bash_script
    path: script.sh

test_resources:
  - type: bash_script
    path: test.sh
  - path: /testData/unit_test_resources/genes.gtf
  - path: /testData/unit_test_resources/wgEncodeCaltechRnaSeqGm12878R1x75dAlignsRep2V2.bam

engines:
- type: docker
  image: ubuntu:22.04
  setup:
    - type: docker
      run: | 
        apt-get update && \
        apt-get install -y build-essential zlib1g wget && \
        wget --no-check-certificate https://github.com/gpertea/stringtie/releases/download/v2.2.1/stringtie-2.2.1.Linux_x86_64.tar.gz && \
        tar -xzf stringtie-2.2.1.Linux_x86_64.tar.gz && \
        cp stringtie-2.2.1.Linux_x86_64/stringtie /usr/local/bin/
runners: 
- type: executable
- type: nextflow
