name: "summarizedexperiment"
info:
  migration_info:
    git_repo: https://github.com/nf-core/rnaseq.git
    paths: [modules/local/summarizedexperiment/main.nf]
    last_sha: 0a1bdcfbb498987643b74e9fccab85ccd9f2a17d
description: Create SummarizedExperiment object from Salmon counts

argument_groups:
- name: "Input"
  arguments:  
  - name: "--tpm_gene"
    type: file
  - name: "--counts_gene"
    type: file
  - name: "--counts_gene_length_scaled"
    type: file
  - name: "--counts_gene_scaled"
    type: file
  - name: "--tpm_transcript"
    type: file
  - name: "--counts_transcript"
    type: file
  - name: "--tx2gene_tsv"
    type: file
    
- name: "Output"
  arguments: 
  - name: "--output"
    type: file
    direction: output
    default: merged_summarizedexperiment

resources:
  - type: bash_script
    path: script.sh
  # copied from https://github.com/nf-core/rnaseq/blob/3.12.0/bin/salmon_summarizedexperiment.r
  - path: summarizedexperiment.r
  
engines:
- type: docker
  image: ubuntu:22.04
  setup:
    - type: apt
      packages: [ r-base, libcurl4-openssl-dev ]
    - type: r
      bioc: [ SummarizedExperiment, tximeta ]
runners: 
- type: executable
- type: nextflow