taf-multiqc

TAFFISH wrapper for MultiQC, a tool for aggregating bioinformatics analysis results across many samples and tools into a single interactive HTML report.

Package Identity

Field	Value
name	multiqc
command	taf-multiqc
version	1.35-r2
kind	tool
container	ghcr.io/taffish/multiqc:1.35-r2
upstream	MultiQC v1.35
runtime version	Python package multiqc==1.35

What This App Provides

This app installs upstream MultiQC 1.35 from PyPI in a Debian-based Python runtime image. It includes the Python dependencies needed for normal HTML report generation and data export, including Plotly, Kaleido, Polars, PyArrow, Pillow, and YAML/config parsing libraries.

The container does not bundle upstream analysis tools such as FastQC, STAR, Salmon, Samtools, aligners, or quantifiers. Run those tools separately, then point MultiQC at their output directories.

Usage

Show the TAFFISH wrapper help:

taf-multiqc --help

Show upstream MultiQC help and version:

taf-multiqc -- --help
taf-multiqc -- --version
taf-multiqc multiqc --help
taf-multiqc multiqc --version

Run MultiQC on the current directory:

taf-multiqc multiqc .

Run MultiQC on several output directories:

taf-multiqc multiqc raw_fastqc star_logs salmon_quant -o multiqc_out

Set a report filename, title, and JSON data output:

taf-multiqc multiqc . --filename sample_qc.html --title "Sample QC" --data-format json --force

Option-leading shorthand also works when the first argument is a MultiQC option:

taf-multiqc -o multiqc_out .

Because TAFFISH command mode treats a first non-option argument as an executable inside the container, do not use taf-multiqc . as the common scan-current- directory form. Use taf-multiqc multiqc . instead.

Command Mode

This is a normal TAFFISH tool app with command mode enabled. The default wrapper is intentionally thin:

<taf-app:container:ghcr.io/taffish/multiqc:1.35-r2>
multiqc ::*ARGV*::

That means you can also run helper commands inside the same container:

taf-multiqc python -c "import multiqc; print(multiqc.__version__)"
taf-multiqc python -c "import plotly, pyarrow, polars"

Outputs

By default, MultiQC writes:

• multiqc_report.html
• multiqc_data/

Use --outdir, --filename, --force, --data-format, --module, --exclude, and --config to control ordinary MultiQC behavior. See upstream MultiQC documentation for the complete CLI and configuration reference.

Platform Notes

The image is intended for native linux/amd64 and linux/arm64 builds. It uses Python 3.11 on Debian bookworm and installs multiqc==1.35 from PyPI.

Kaleido runtime libraries and fonts are included so flat Plotly image export can work in the container. MultiQC 1.35 pins kaleido==0.2.1, so Plotly may print a Kaleido deprecation warning during image export even though the smoke PNG export passes. PDF or LaTeX-heavy report export paths are not the main smoke-covered workflow for this app.

Smoke Coverage

The app smoke metadata checks:

• the multiqc, python, and python3 commands exist;
• the installed Python package version is exactly 1.35;
• upstream multiqc --version and multiqc --help run;
• core Python dependencies import successfully;
• a minimal custom-content report is generated with HTML and JSON data output;
• Plotly/Kaleido can write a small PNG image.

These checks validate container packaging and basic report generation. They do not replace full scientific validation of every MultiQC parser module.

Upstream

• Source: https://github.com/MultiQC/MultiQC
• Documentation: https://docs.seqera.io/multiqc
• Website: https://seqera.io/multiqc/
• License: GPL-3.0-or-later
• Citation: Ewels et al. 2016, doi: 10.1093/bioinformatics/btw354, PMID: 27312411