Quality Control Nodes

QC nodes assess the quality of raw and processed data. Run them early and often — catching a bad library prep before alignment saves hours of compute.

FastQC

Computes per-base quality, GC content, adapter contamination, and duplication metrics for raw reads.

Inputs: reads: FASTQ Outputs: report: Report, data: Directory

MultiQC

Aggregates reports from many tools (FastQC, alignment stats, dedup metrics) into a single interactive HTML report.

Inputs: reports: List<Report | Directory> Outputs: report: Report

Connect every QC-producing node’s output into a single MultiQC node to get one consolidated dashboard for the whole run.

fastp / Trim Galore (trimming)

Adapter and quality trimming. Produces cleaned reads plus a QC report.

Inputs: reads: FASTQ Outputs: trimmed: FASTQ, report: Report

Typical QC subgraph

[FASTQ Input] → [FastQC]  ─┐
       │                   ├→ [MultiQC report]
       └→ [fastp] → [FastQC] ┘  (post-trim QC)

See also

• Alignment nodes
• Your First Workflow