name: tgMap
version: 0.0.2
output_asset_class: tgMap
description:
  Transcript to gene map file, containing two columns mapping of each transcript
  present in the reference to the corresponding gene.
input_files: {}
input_params: {}
input_assets:
  salmon_partial_sa_index:
    asset_class: salmon_partial_sa_index
    default: salmon_partial_sa_index
    description: partial salmon index asset
docker_image: null
command_templates:
  - grep '^>' {{values.genome_folder}}/{{values.assets["salmon_partial_sa_index"].seek_keys_dict["salmon_partial_sa_index"]}}/gentrome.fa | cut -d ' ' -f 1,7 | tr -s ' ' '\t' | sed 's/[>'gene_symbol:']//g' > {{values.output_folder}}/{{values.genome_digest}}_txp2gene.tsv
default_asset: "default"
tags:
- annotation
- rna-seq
- transcript-gene-map
outputs:
- pattern: '*_txp2gene.tsv'
  description: Transcript to gene mapping TSV file
resources:
  memory: 2GB
  disk: 1GB
  time: 30m
test:
  commands:
  - test -f {output_dir}/{genome}_txp2gene.tsv
metadata:
  author: nsheff
  created: '2026-05-20'
  license: BSD-2-Clause