name: hisat2_index
version: 0.0.3
output_asset_class: hisat2_index
description: Genome index for HISAT2, produced with hisat2-build
input_files: {}
input_params: {}
input_assets:
  fasta:
    asset_class: fasta
    default: fasta
    description: fasta asset for genome
docker_image: quay.io/biocontainers/hisat2:2.2.2--h503566f_0
command_templates:
  - hisat2-build {{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: hisat2-build --version 2>/dev/null | sed -nE 's/^hisat2-build version ([0-9][^ ]*).*/\1/p' | head -1
default_asset: "{{values.custom_seek_keys.version}}"

# --- Additive non-runtime metadata (ignored by the builder) ---
tags:
- alignment
- rna-seq
- spliced-alignment
outputs:
- pattern: '*.ht2'
  description: HISAT2 index files
- pattern: '*.ht2l'
  description: HISAT2 large index files (for genomes >= 4Gbp)
test:
  commands:
  - test -f {output_dir}/{genome}.1.ht2 || test -f {output_dir}/{genome}.1.ht2l
resources:
  memory: 8GB
  disk: 10GB
  time: 2h
metadata:
  author: nsheff
  created: '2026-05-20'
  license: BSD-2-Clause