name: bowtie1_index
version: 0.0.2
output_asset_class: bowtie1_index
description: |
  Genome index for bowtie, produced with bowtie-build.
  Creates index files used by bowtie for short-read alignment.
input_files: null
input_params:
  threads:
    description: Number of threads to use
    default: 1
input_assets:
  fasta:
    asset_class: fasta
    description: fasta asset for genome
    default: fasta
docker_image: quay.io/biocontainers/bowtie:1.3.1--hb82490e_11
command_templates:
  - bowtie-build --threads {{values.params["threads"]}} {{values.genome_folder}}/{{values.assets["fasta"].seek_keys_dict["fasta"]}} {{values.output_folder}}/{{values.genome_digest}}
custom_seek_keys:
  version: bowtie-build --version | awk 'NR==1{print $3}'
default_asset: "{{values.custom_seek_keys.version}}"

tags:
- alignment
- dna-seq
- short-read
outputs:
- pattern: '*.ebwt'
  description: Bowtie1 index files
test:
  commands:
  - test -f {output_dir}/{genome}.1.ebwt
resources:
  memory: 8GB
  disk: 10GB
  time: 2h
metadata:
  author: nsheff
  created: '2026-05-20'
  license: BSD-2-Clause