name: salmon_index
version: 0.0.2
output_asset_class: salmon_index
description: Transcriptome index for salmon, produced with salmon index
input_files: {}
input_params:
  threads:
    default: "8"
    description: Number of threads to use for parallel computing
  kmer:
    default: "31"
    description: The length of kmer to use to create the indices
input_assets:
  fasta_txome:
    asset_class: fasta
    default: fasta_txome
    description: fasta asset for transcriptome
docker_image: quay.io/biocontainers/salmon:2.3.4--hfa8f182_0
command_templates:
  - salmon index -t {{values.genome_folder}}/{{values.assets["fasta_txome"].seek_keys_dict["fasta"]}} -i {{values.output_folder}} -k {{values.params["kmer"]}} -p {{values.params["threads"]}}
custom_seek_keys:
  version: salmon --version | awk '{print $2}'
default_asset: "{{values.custom_seek_keys.version}}"
tags:
- quantification
- rna-seq
- pseudoalignment
outputs:
- pattern: '*.json'
  description: Salmon index metadata files
- pattern: seq.bin
  description: Salmon sequence binary
- pattern: pos.bin
  description: Salmon position binary
resources:
  memory: 8GB
  disk: 10GB
  time: 1h
test:
  commands:
  - test -d {output_dir}
  - test -f {output_dir}/seq.bin
metadata:
  author: nsheff
  created: '2026-05-20'
  license: BSD-2-Clause