47 lines
1.0 KiB
YAML
Executable File
47 lines
1.0 KiB
YAML
Executable File
# Gene Identify Skill Configuration
|
|
|
|
skill:
|
|
name: gene-identify
|
|
version: "1.0.0"
|
|
description: "基因家族成员鉴定 - HMMER为必选；当config.xlsx声明参考家族蛋白时追加BLAST证据"
|
|
author: "bbav2-team"
|
|
|
|
input:
|
|
protein_fasta: null # 必需: 蛋白质FASTA文件路径
|
|
hmm_file: null # 必需: HMM模型文件路径
|
|
species_code: null # 必需: 物种代码
|
|
|
|
parameters:
|
|
hmmer:
|
|
evalue: 1e-5
|
|
coverage: 0.3
|
|
cpu: 4
|
|
blast:
|
|
evalue: 1e-5
|
|
max_target_seqs: 10
|
|
verify: true
|
|
database_role: target_proteome
|
|
query_role: reference_family_pep
|
|
candidate_id_column: sseqid
|
|
domain:
|
|
min_domain_length: 20
|
|
merge_overlap: 0.3
|
|
|
|
output:
|
|
format: ["csv", "gff3", "pdf"]
|
|
report_template: "templates/report.md.j2"
|
|
include_reproducibility: true
|
|
|
|
dependencies:
|
|
conda:
|
|
channels:
|
|
- bioconda
|
|
- conda-forge
|
|
packages:
|
|
- hmmer=3.3.2
|
|
- blast=2.13.0
|
|
- biopython=1.81
|
|
- pandas=2.0.0
|
|
- matplotlib=3.7.0
|
|
- seaborn=0.12.0
|