sarek

What problem does it solve?

nf-core/sarek automates germline and somatic variant analysis so researchers do not need to manually assemble complex Nextflow commands, parameter sets, and reference inputs for every sequencing project.

Core Features & Use Cases

• End-to-end variant calling: Supports whole-genome, whole-exome, targeted, tumor-normal, and tumor-only workflows from raw reads through annotated outputs.
• Strict parameter validation: Uses a pinned release schema to constrain inputs, required flags, allowed values, and file formats before the run starts.
• Practical research use: Helps bioinformatics teams standardize sample sheet-driven analyses, reproduce prior runs, and choose the right tools for alignment, deduplication, calling, and annotation.

Quick Start

Ask for a complete nf-core/sarek run plan for my samplesheet, including the required parameters, recommended step, and the exact nfclaw command for my chosen sequencing scenario.