39 lines
1.0 KiB
YAML
Executable File
39 lines
1.0 KiB
YAML
Executable File
# Synteny Skill Configuration
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skill:
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name: synteny
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version: "1.0.0"
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description: "共线性分析 - MCScanX/JCVI"
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author: "bbav2-team"
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input:
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query_gff: null # 查询物种代表转录本GFF3；优先使用 {species}_final.gff3 / {species}.gff3
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query_pep: null # 查询物种代表转录本蛋白FASTA；优先使用 {species}.pep.fasta
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ref_gff: null # 参考物种代表转录本GFF3
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ref_pep: null # 参考物种代表转录本蛋白FASTA
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parameters:
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representative_transcript_required: true # MCScanX输入应每个基因座一个代表转录本；原始多转录本文件仅作回退
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evalue: 1e-10
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max_target_seqs: 5
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minspan: 10
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blast_method: "blastp" # blastp or diamond
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output:
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format: ["txt", "png", "pdf"]
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report_template: "templates/report.md.j2"
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include_reproducibility: true
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dependencies:
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conda:
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channels:
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- bioconda
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- conda-forge
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packages:
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- blast=2.13.0
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- diamond=2.1.8
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- mcscanx
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- jcvi=1.3.0
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- biopython=1.81
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- pandas=2.0.0
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- matplotlib=3.7.0 |