Pipelines

Pipelines let you connect analysis steps visually so that the output from one step becomes the input for the next one.

Use pipelines when you want to repeat a workflow, avoid manual file handoffs, or combine built-in tools, .lia plugins, and AI Tools in one place.

What a pipeline contains

A pipeline is made of nodes and connections:

• Input nodes provide starting files or values.
• Tool nodes run built-in tools, .lia plugins, or AI Tools.
• Logic nodes help control simple branching or conditional behavior.
• Connections pass compatible outputs into later inputs.

Each node exposes only the inputs that make sense for that tool. File pickers are filtered by compatible format whenever possible.

Running a pipeline

1. Open Pipeline from the sidebar.
2. Add the tools or plugins you want to use.
3. Connect outputs to compatible inputs.
4. Fill in required fields.
5. Click Run pipeline.

While the pipeline is running, the active pipeline is disabled to prevent accidental edits. Other pipelines and unrelated pages should remain usable.

Jobs and Results

Long-running steps appear in Jobs while they run. When the pipeline finishes, the completed run appears in Results with:

• the pipeline name;
• each step that ran;
• logs and errors;
• output files;
• metrics and summaries;
• provenance for tools and AI Models.

If a step fails, Liatir keeps the logs and shows which part of the pipeline failed so you can fix the input or settings and run again.

Example workflows

FASTQ quality control

1. Start from FASTQ files in Data.
2. Run FastQC.
3. Run fastp to trim reads.
4. Add trimmed files back to Data or pass them to the next step.

Variant filtering

1. Start from a VCF or BCF file.
2. Run BCFtools stats to inspect the callset.
3. Run BCFtools filter with a quality expression.
4. Review the filtered VCF in Results.

AI-assisted workflows

1. Install a compatible AI Model.
2. Add an AI Tool to the pipeline.
3. Select the model inside the tool.
4. Connect the generated output to viewers, reports, or later tools.

Example AI pipelines:

• .h5ad file to CellTypist Annotation to label summary.
• FASTA plus VCF to Genomic Variant Effect to BED track.
• DNA window to Regulatory Prediction to genome viewer.
• Protein FASTA to Protein Structure Prediction to 3D viewer.

Read Local AI for bioinformatics before interpreting AI outputs.

Saving and reusing workflows

Pipelines are meant to be reusable. A saved workflow keeps its structure and settings so you can return to it later, adjust inputs, and run it again.

For custom steps, use .lia plugins. A plugin can wrap a script or command-line tool through the Liatir API bridge and still behave like a normal node in the pipeline.