name: bowtie2_index
version: 0.0.2
output_asset_class: bowtie2_index
description: |
  Genome index for bowtie2, produced with bowtie2-build.
  Creates the FM-index files used by bowtie2 for fast and
  memory-efficient alignment of short reads.
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/bowtie2:2.5.5--ha27dd3b_0
command_templates:
  - bowtie2-build --threads {{values.params["threads"]}} {{values.genome_folder}}/{{values.assets["fasta"].seek_keys_dict["fasta"]}} {{values.output_folder}}/{{values.genome_digest}}
custom_seek_keys:
  # sed -E, not grep -P: the biocontainers image's grep is BusyBox (no -P),
  # and the whole pipeline runs inside that one image now.
  version: bowtie2-build --version 2>/dev/null | sed -nE 's/^.*bowtie2-build-[sl] version ([0-9]+\.[0-9]+(\.[0-9]+)?).*/\1/p;s/^.*bowtie2-([0-9]+\.[0-9]+(\.[0-9]+)?) .*/\1/p' | head -1
default_asset: "{{values.custom_seek_keys.version}}"

tags:
- alignment
- dna-seq
- short-read
outputs:
- pattern: '*.bt2'
  description: Bowtie2 index files (standard, for genomes < 4Gbp)
- pattern: '*.bt2l'
  description: Bowtie2 large index files (for genomes >= 4Gbp)
test:
  commands:
  - test -f {output_dir}/{genome}.1.bt2 || test -f {output_dir}/{genome}.1.bt2l
resources:
  memory: 8GB
  disk: 10GB
  time: 2h
metadata:
  author: nsheff
  created: '2026-05-20'
  license: BSD-2-Clause