name: "preprocess_transcripts_fasta"
info:
  migration_info:
    git_repo: https://github.com/nf-core/rnaseq.git
    paths: [modules/local/preprocess_transcripts_fasta_gencode.nf]
    last_sha: 0a1bdcfbb498987643b74e9fccab85ccd9f2a17d
description: |
  Process transcripts FASTA if GTF file is GENOCODE format

argument_groups:
- name: "Input"
  arguments:
  - name: "--transcript_fasta"
    type: file 
    required: true
    description: Path of transcripts FASTA file

- name: "Output"
  arguments:    
  - name: "--output"
    type: file
    direction: output
    required: true
    description: Path of processed output FASTA file.

resources:
  - type: bash_script
    path: script.sh

test_resources:
  - type: bash_script
    path: test.sh
  - path: /testData/minimal_test/reference/transcriptome.fasta
  
engines:
  - type: docker
    image: ubuntu:22.04
runners:
  - type: executable
  - type: nextflow