name: tallymer_index
version: 0.0.2
output_asset_class: tallymer_index
description:
  Indexed k-mers for a given enhanced suffix array at a fixed value of
  k
input_files: {}
input_params:
  mersize:
    default: "30"
    description: The mer size.
  minocc:
    default: "2"
    description: The minimum occurrence number for the mers to index.
input_assets:
  suffixerator_index:
    asset_class: suffixerator_index
    default: suffixerator_index
    description: enhanced suffix array index for genome
  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 tallymer mkindex -v -counts -pl \
    -mersize {{values.params["mersize"]}} \
    -minocc {{values.params["minocc"]}} \
    -indexname {{values.output_folder}}/{{values.genome_digest}}.tal_{{values.params["mersize"]}} \
    -esa {{values.genome_folder}}/{{values.assets["suffixerator_index"].seek_keys_dict["esa"]}}
  - |
    gt tallymer search -output qseqnum qpos -strand fp \
    -tyr {{values.output_folder}}/{{values.genome_digest}}.tal_{{values.params["mersize"]}} \
    -q {{values.genome_folder}}/{{values.assets["fasta"].seek_keys_dict["fasta"]}} \
    > {{values.output_folder}}/{{values.genome_digest}}.tal_{{values.params["mersize"]}}.gtTxt
custom_seek_keys:
  version: "gt tallymer --version | awk 'NR==1{print $4}'"
default_asset: "{{values.custom_seek_keys.version}}"
tags:
- index
- k-mer
- genomics
outputs:
- pattern: '*.tal_*'
  description: Tallymer index files
- pattern: '*.tal_*.gtTxt'
  description: Tallymer search output
resources:
  memory: 8GB
  disk: 10GB
  time: 2h
test:
  commands:
  - test -f {output_dir}/{genome}.tal_{mersize}.gtTxt
metadata:
  author: nsheff
  created: '2026-05-20'
  license: BSD-2-Clause