name: salmon_sa_index
version: 0.0.2
output_asset_class: salmon_sa_index
description:
  Transcriptome index for salmon, produced with salmon index using selective
  alignment method. Improves quantification accuracy compared to the regular 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:
    asset_class: fasta
    default: fasta
    description: fasta asset for genome
  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:
  - grep '^>' {{values.genome_folder}}/{{values.assets["fasta"].seek_keys_dict["fasta"]}} | cut -d ' ' -f 1 > {{values.output_folder}}/decoys.txt
  - sed -i.bak -e 's/>//g' {{values.output_folder}}/decoys.txt
  - rm {{values.output_folder}}/decoys.txt.bak
  - cat {{values.genome_folder}}/{{values.assets["fasta_txome"].seek_keys_dict["fasta"]}} {{values.genome_folder}}/{{values.assets["fasta"].seek_keys_dict["fasta"]}} > {{values.output_folder}}/gentrome.fa
  - salmon index -t {{values.output_folder}}/gentrome.fa -d {{values.output_folder}}/decoys.txt -i {{values.output_folder}} -k {{values.params["kmer"]}} -p {{values.params["threads"]}}
  - rm {{values.output_folder}}/gentrome.fa {{values.output_folder}}/decoys.txt
custom_seek_keys:
  version: salmon --version | awk '{print $2}'
default_asset: "{{values.custom_seek_keys.version}}"
tags:
- quantification
- rna-seq
- pseudoalignment
- selective-alignment
outputs:
- pattern: '*.json'
  description: Salmon index metadata files
- pattern: seq.bin
  description: Salmon sequence binary
- pattern: pos.bin
  description: Salmon position binary
resources:
  memory: 16GB
  disk: 20GB
  time: 2h
test:
  commands:
  - test -d {output_dir}
  - test -f {output_dir}/seq.bin
metadata:
  author: nsheff
  created: '2026-05-20'
  license: BSD-2-Clause