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Updated Oct 19, 2026

Utilities

Combine QC logs into one MultiQC report

multiqc-report is an offline reporting node for existing QC logs.

Agent
Compare existing sample metricsCombine supported QC modulesRetain parsed report data

overview

What multiqc-report does

Supply a folder of existing quality-control logs and receive a MultiQC HTML report with native parsed data.

Choose comma-separated modules from fastqc, fastp, cutadapt, samtools and kallisto. fastqc is the default. Input configuration files are ignored; this operation aggregates existing logs and does not run the underlying QC programs.

Input is limited to 200 files and 50 MiB total, with a 300-second native timeout. No custom modules, AI analysis or remote calls are exposed. The source logs determine which metrics and samples are available.

This packaged operation uses 1.35. Upstream license: GPL-3.0. The linked source identifies the actual program; this page documents the adapter's exposed contract.

source github.com/MultiQC/MultiQC/tree/v1.35

use cases

Where multiqc-report fits

Compare existing sample metrics

Compare sample metrics that already exist in supported logs.

Combine supported QC modules

Select only the exposed QC log modules.

Retain parsed report data

Keep native parsed data beside the HTML report.

reference

multiqc-report inputs and flags

2 inputs
NameTypeFlagDescription
sourceFOLDER--sourceFolder of QC logs, at most 200 files and 50 MiB total.
modulesSTRING--modulesComma-separated modules: fastqc, fastp, cutadapt, samtools, kallisto (default fastqc).

Showing key inputs. multiqc-report exposes 2 inputs in total.

example

Run multiqc-report

multiqc-report · command
python3 /app/run.py --source ./source --modules fastqc ./output

guidance

Choosing multiqc-report

Use MultiQC after producing compatible QC logs. Generate missing logs with the appropriate QC tool first; aggregation cannot measure quality from raw reads by itself.

faq

multiqc-report questions

source: Folder of QC logs, at most 200 files and 50 MiB total. modules: Comma-separated modules: fastqc, fastp, cutadapt, samtools, kallisto (default fastqc).

HTML report and parsed data. Choose comma-separated modules from fastqc, fastp, cutadapt, samtools and kallisto. fastqc is the default. Input configuration files are ignored; this operation aggregates existing logs and does not run the underlying QC programs.

Input is limited to 200 files and 50 MiB total, with a 300-second native timeout. No custom modules, AI analysis or remote calls are exposed. The source logs determine which metrics and samples are available.

Use MultiQC after producing compatible QC logs. Generate missing logs with the appropriate QC tool first; aggregation cannot measure quality from raw reads by itself.

The public image repository includes download instructions for this version and a separate source/notices bundle. Its overview provides an immutable ORAS command, the expected bundle checksum and pinned upstream source directions. The bundle contains the original build recipe, runtime sources and retained component license notices. Image, source and license notice downloads.

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Run multiqc-report yourself

The saved synthetic FastQC-log check verified two samples with 100 and 250 reads and GC percentages 40 and 55. It also verified that an input MultiQC configuration was ignored. The full report is not retained as a page sample. The command shows the container entrypoint with example paths.

Open multiqc-report in the libraryBuild a workflow with it

Facts on this page come from the live Trickest tool library.