name: fasta_txome
version: 0.0.2
output_asset_class: fasta
description:
  cDNA sequences in the FASTA format, indexed FASTA (produced with samtools
  index) and chromosome sizes file
input_files:
  fasta_txome:
    description: A taxome FASTA file. Gzipped or not.
input_params: {}
input_assets: {}
docker_image: quay.io/biocontainers/samtools:1.24--h9dcdb79_1
command_templates:
  - cp {{values.files["fasta_txome"]}} {{values.output_folder}}/{{values.genome_digest}}.fa.gz
  # `file` isn't in the samtools biocontainers image; `gzip -t` detects a real
  # gzip stream without it.
  - if gzip -t {{values.output_folder}}/{{values.genome_digest}}.fa.gz >/dev/null 2>&1 ; then gzip -df {{values.output_folder}}/{{values.genome_digest}}.fa.gz ; else mv {{values.output_folder}}/{{values.genome_digest}}.fa.gz {{values.output_folder}}/{{values.genome_digest}}.fa ; fi
  - samtools faidx {{values.output_folder}}/{{values.genome_digest}}.fa
  - cut -f 1,2 {{values.output_folder}}/{{values.genome_digest}}.fa.fai > {{values.output_folder}}/{{values.genome_digest}}.chrom.sizes
  - cat {{values.output_folder}}/{{values.genome_digest}}.fa | samtools dict -o {{values.output_folder}}/{{values.genome_digest}}.dict
custom_seek_keys:
  version: "samtools --version-only | awk -F+ '{print $1}'"
default_asset: "samtools-{{values.custom_seek_keys.version}}"

# --- Additive non-runtime metadata (ignored by the builder) ---
tags:
- reference
- sequence
- transcriptome
outputs:
- pattern: '*.fa'
  description: Transcriptome FASTA file
- pattern: '*.fa.fai'
  description: FASTA index file
- pattern: '*.chrom.sizes'
  description: Chromosome sizes file
test:
  commands:
  - test -f {output_dir}/{genome}.fa
  - test -f {output_dir}/{genome}.fa.fai
  - test -f {output_dir}/{genome}.chrom.sizes
resources:
  memory: 4GB
  disk: 10GB
  time: 1h
metadata:
  author: nsheff
  created: '2026-05-20'
  license: BSD-2-Clause