name: "tximport"
info:
  migration_info:
    git_repo: https://github.com/nf-core/rnaseq.git
    paths: [modules/local/tximport/main.nf]
    last_sha: 489bcb4efdc7bd58839b22b0360d26b4d80b87a8
description: Get dataframe linking transcript ID, gene ID, and gene name

argument_groups:
- name: "Input"
  arguments:  
  - name: "--quant_results"
    type: file
    multiple: true
    multiple_sep: ","
  - name: "--tx2gene_tsv"
    type: file
  - name: "--quant_type"
    type: string
    description: Method used for quantification
    choices: ["salmon", "kallisto"]
    
- name: "Output"
  arguments:   
  - name: "--tpm_gene"
    type: file
    direction: output
    default: merged.gene_tpm.tsv
  - name: "--counts_gene"
    type: file
    direction: output
    default: merged.gene_counts.tsv
  - name: "--counts_gene_length_scaled"
    type: file
    direction: output
    default: merged.gene_counts_length_scaled.tsv
  - name: "--counts_gene_scaled"
    type: file
    direction: output
    default: merged.gene_counts_scaled.tsv
  - name: "--lengths_gene"
    type: file
    direction: output
    default: merged.gene_length.tsv
  - name: "--tpm_transcript"
    type: file
    direction: output
    default: merged.transcript_tpm.tsv
  - name: "--counts_transcript"
    type: file
    direction: output
    default: merged.transcript_counts.tsv
  - name: "--lengths_transcript"
    type: file
    direction: output
    default: merged.transcript_length.tsv

resources:
  - type: bash_script
    path: script.sh
  # copied from https://github.com/nf-core/rnaseq/blob/3.14.0/bin/tximport.r
  - path: tximport.r
  
engines:
- type: docker
  image: ubuntu:22.04
  setup:
    - type: apt
      packages: [ r-base, libcurl4-openssl-dev, libssl-dev, libxml2-dev ]
    - type: r      
      bioc: [ SummarizedExperiment, tximport, tximeta ]
      cran: [ jsonlite ]
runners: 
- type: executable
- type: nextflow