name: "cat_additional_fasta"
info:
  migration_info:
    git_repo: https://github.com/nf-core/rnaseq.git
    paths: [modules/local/cat_additional_fasta.nf]
    last_sha: 0a1bdcfbb498987643b74e9fccab85ccd9f2a17d
description: |
  Concatenate addional fasta file to reference FASTA and GTF files.

argument_groups:
- name: "Input"
  arguments: 
  - name: "--fasta"
    type: file 
    required: true
    description: Path to FASTA genome file.
  - name: "--gtf"
    type: file
    description: Path to GTF annotation file.
  - name: "--additional_fasta"
    type: file
    description: FASTA file to concatenate to genome FASTA file e.g. containing spike-in sequences.
  - name: "--biotype"
    type: string
    description: Biotype value to use when appending entries to GTF file when additional fasta file is provided.

- name: "Output"
  arguments: 
  - name: "--fasta_output"
    type: file
    direction: output
    description: Concatenated FASTA file.
  - name: "--gtf_output"
    type: file
    direction: output
    description: Concatenated GTF file.

resources:
  - type: python_script
    path: script.py

test_resources:
  - type: bash_script
    path: test.sh
  - path: /testData/minimal_test/reference/genome.fasta
  - path: /testData/minimal_test/reference/genes.gtf.gz
  - path: /testData/minimal_test/reference/gfp.fa.gz
  
engines:
  - type: docker
    image: python 
runners:
  - type: executable
  - type: nextflow