Workflow Templates

Workflow templates are pre-built analysis pipelines curated by the Biomni Lab team. They help you get started quickly with common bioinformatics tasks.

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Using a Template

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From the Chat Input

Click the + Workflow button in the chat input area to browse available templates:

1. Click + Workflow next to the chat input
2. Browse templates by category or search
3. Click a template to see its description and requirements
4. Click Use Template to apply it
5. Provide the required input files when prompted

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From Suggested Templates

When you start a new task, relevant workflow templates appear in the chat area based on common use cases:

1. Click on a template to see what it does
2. Click Use Template to apply it
3. Provide the required input files when prompted

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Template Examples

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RNA-seq Differential Expression

Performs full RNA-seq analysis from raw reads:

1. Quality control with FastQC
2. Alignment with STAR
3. Quantification with featureCounts
4. Differential expression with DESeq2
5. Visualization with volcano plots and heatmaps

Required inputs: Paired-end FASTQ files, sample metadata

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Single-cell Clustering

Analyzes single-cell RNA-seq data:

1. Quality filtering
2. Normalization and scaling
3. Dimensionality reduction (PCA, UMAP)
4. Clustering
5. Marker gene identification

Required inputs: Count matrix or 10x Genomics output

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Variant Calling

Identifies genetic variants from sequencing data:

1. Alignment to reference genome
2. Mark duplicates
3. Base quality recalibration
4. Call variants with GATK
5. Variant annotation with VEP

Required inputs: FASTQ files, reference genome