47 lines
873 B
YAML
Executable File
47 lines
873 B
YAML
Executable File
# TFBS Prediction Skill Configuration
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skill:
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name: tfbs-prediction
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version: "1.0.0"
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description: "TF binding-site prediction with promoter extraction and MEME Suite FIMO"
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author: "bbav5-team"
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input:
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gff3: null
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genome_fasta: null
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gene_ids: null
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parameters:
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upstream_length: 2000
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motif_db_mode: auto
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fimo_pvalue: 0.0001
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fimo_qvalue: 0.05
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background_mode: none
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max_nearest_rank: order
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top_motifs: 30
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scan_both_strands: true
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cpu: 4
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output:
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manifest: "{prefix}.tfbs.manifest.json"
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tables:
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- "{prefix}.tfbs.sites.tsv"
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- "{prefix}.tfbs.enrichment.tsv"
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- "{prefix}.tfbs.gene_motif_matrix.tsv"
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figures:
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- "{prefix}.tfbs.*.png"
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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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- meme
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- seqkit
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- gffread
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- pandas
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- scipy
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- matplotlib
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- seaborn
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