name: kallisto_index
version: 0.0.2
output_asset_class: kallisto_index
description: Genome index for kallisto, produced with kallisto index
input_files: {}
input_params: {}
input_assets:
  fasta_txome:
    asset_class: fasta
    default: fasta_txome
    description: fasta asset for transcriptome
docker_image: quay.io/biocontainers/kallisto:0.52.0--h13ff97a_0
command_templates:
  - kallisto index -i {{values.output_folder}}/{{values.genome_digest}}_kallisto_index.idx {{values.genome_folder}}/{{values.assets["fasta_txome"].seek_keys_dict["fasta"]}}
custom_seek_keys:
  version: "kallisto version | awk '{print $3}'"
default_asset: "{{values.custom_seek_keys.version}}"
tags:
- quantification
- rna-seq
- pseudoalignment
outputs:
- pattern: '*_kallisto_index.idx'
  description: Kallisto index file
resources:
  memory: 8GB
  disk: 5GB
  time: 1h
test:
  commands:
  - test -f {output_dir}/{genome}_kallisto_index.idx
metadata:
  author: nsheff
  created: '2026-05-20'
  license: BSD-2-Clause