name: suffixerator_index
version: 0.0.2
output_asset_class: suffixerator_index
description:
  Enhanced suffix array index for genomes using gt (GenomeTools) suffixerator
  program
input_files: {}
input_params:
  memlimit:
    default: 8
    description: The maximum amount of memory available to be used during index
      construction.
input_assets:
  fasta:
    asset_class: fasta
    default: fasta
    description: fasta asset for genome
docker_image: quay.io/biocontainers/genometools-genometools:1.6.6--py311h21ec246_1
command_templates:
  - gt suffixerator -dna -pl -tis -suf -lcp -v -showprogress -memlimit {{values.params["memlimit"]}}GB -db {{values.genome_folder}}/{{values.assets["fasta"].seek_keys_dict["fasta"]}} -indexname {{values.output_folder}}/{{values.genome_digest}}.sft
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: gt suffixerator --version 2>/dev/null | sed -nE 's/^.*\(GenomeTools\) ([0-9][^ ]*).*/\1/p' | head -1
default_asset: "{{values.custom_seek_keys.version}}"
tags:
- index
- suffix-array
- genomics
outputs:
- pattern: '*.sft.*'
  description: Enhanced suffix array index files
resources:
  memory: 8GB
  disk: 10GB
  time: 2h
test:
  commands:
  - ls {output_dir}/{genome}.sft.* >/dev/null 2>&1
metadata:
  author: nsheff
  created: '2026-05-20'
  license: BSD-2-Clause