name: star_index
version: 0.0.2
output_asset_class: star_index
description: Genome index for STAR RNA-seq aligner, produced with STAR --runMode genomeGenerate
input_files: {}
input_params:
  threads:
    default: "8"
    description: Number of threads to use for parallel computing
input_assets:
  fasta:
    asset_class: fasta
    default: fasta
    description: fasta asset for genome
docker_image: quay.io/biocontainers/star:2.7.11b--h5ca1c30_8
command_templates:
  - mkdir -p {{values.output_folder}}
  - STAR --runThreadN {{values.params["threads"]}} --runMode genomeGenerate --genomeDir {{values.output_folder}} --genomeFastaFiles {{values.genome_folder}}/{{values.assets["fasta"].seek_keys_dict["fasta"]}}
custom_seek_keys:
  version: "STAR --version"
default_asset: "{{values.custom_seek_keys.version}}"
tags:
- alignment
- rna-seq
- spliced-alignment
outputs:
- pattern: Genome
  description: STAR genome index binary
- pattern: SA
  description: STAR suffix array
- pattern: SAindex
  description: STAR suffix array index
- pattern: chrName.txt
  description: Chromosome names
- pattern: chrLength.txt
  description: Chromosome lengths
resources:
  memory: 32GB
  disk: 30GB
  time: 2h
test:
  commands:
  - test -f {output_dir}/Genome
  - test -f {output_dir}/SA
  - test -f {output_dir}/SAindex
metadata:
  author: nsheff
  created: '2026-05-20'
  license: BSD-2-Clause