name	multiqc
description	Use when you need to aggregate quality control reports from multiple bioinformatics tools into a single HTML report
disable-model-invocation	true
user-invocable	true

multiqc

Aggregate many per-sample QC or analysis reports into one HTML dashboard.
Summarize outputs from FastQC, cutadapt, aligners, quantifiers, and many other tools.
Use it after per-sample processing is done, not as a first-pass QC tool.
Best for cohort-level review and sample-to-sample comparison.

# 1) Scan the current analysis directory
multiqc .

# 2) Write report into a dedicated output directory
multiqc results -o multiqc_out -n project_multiqc.html

# 3) Limit or exclude modules
multiqc results -m fastqc -m cutadapt -e star

# 4) Prefix sample names with directory names to reduce collisions
multiqc results -d

Run per-sample QC and analysis tools first.
Point MultiQC at the project results tree or a curated file list.
Review sample naming, module detection, and missing-module warnings before trusting the report.
Archive the HTML plus parsed data directory if the summary will be cited or shared.

MultiQC only summarizes logs it recognizes; if upstream tools did not emit report files, there is nothing to aggregate.
Re-running in the same output location often needs -f/--force.
Sample name collisions can silently confuse interpretation; use -d, -s, or renaming options when needed.
If the report looks suspiciously sparse, check whether modules were excluded or whether files were ignored by glob patterns.

来源信息