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Merge pull request #1722 from RaheelSyedAhmed/multiqc-1.35
Multiqc 1.35
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‎README.md‎

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| [MMseqs2](https://hub.docker.com/r/staphb/mmseqs2) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/mmseqs2)](https://hub.docker.com/r/staphb/mmseqs2) | <details><summary>Click to see all versions</summary> <ul><li>[17-b804f](./build-files/mmseqs2/17-b804f/)</li><li>[18-8cc5c](./build-files/mmseqs2/18-8cc5c/)</li></ul> </details> | https://github.com/soedinglab/MMseqs2 |
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| [mob-suite](https://github.com/phac-nml/mob-suite) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/mob-suite)](https://hub.docker.com/r/staphb/mob-suite) | <details><summary>Click to see all versions</summary> <ul><li>[3.1.9](./build-files/mob-suite/3.1.9/)</li></ul> </details> | https://github.com/phac-nml/mob-suite |
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| [Mugsy](https://hub.docker.com/r/staphb/mugsy) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/mugsy)](https://hub.docker.com/r/staphb/mugsy) | <details><summary>Click to see all versions</summary> <ul><li>[1r2.3](./build-files/mugsy/1r2.3/)</li></ul> </details> | http://mugsy.sourceforge.net/ |
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| [MultiQC](https://hub.docker.com/r/staphb/multiqc) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/multiqc)](https://hub.docker.com/r/staphb/multiqc) | <details><summary>Click to see all versions</summary> <ul><li>[1.7](./build-files/multiqc/1.7/)</li><li>[1.8](./build-files/multiqc/1.8/)</li><li>[1.18](./build-files/multiqc/1.18/)</li><li>[1.19](./build-files/multiqc/1.19/)</li><li>[1.22.2](./build-files/multiqc/1.22.2/)</li><li>[1.22.3](./build-files/multiqc/1.22.3/)</li><li>[1.25](./build-files/multiqc/1.25/)</li><li>[1.26](./build-files/multiqc/1.26/)</li><li>[1.27.1](./build-files/multiqc/1.27.1/)</li><li>[1.28](./build-files/multiqc/1.28/)</li><li>[1.30](./build-files/multiqc/1.30/)</li><li>[1.31](./build-files/multiqc/1.31/)</li><li>[1.33](./build-files/multiqc/1.33/)</li><li>[1.34](./build-files/multiqc/1.34/)</li></ul> </details> | https://github.com/MultiQC/MultiQC |
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| [MultiQC](https://hub.docker.com/r/staphb/multiqc) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/multiqc)](https://hub.docker.com/r/staphb/multiqc) | <details><summary>Click to see all versions</summary> <ul><li>[1.7](./build-files/multiqc/1.7/)</li><li>[1.8](./build-files/multiqc/1.8/)</li><li>[1.18](./build-files/multiqc/1.18/)</li><li>[1.19](./build-files/multiqc/1.19/)</li><li>[1.22.2](./build-files/multiqc/1.22.2/)</li><li>[1.22.3](./build-files/multiqc/1.22.3/)</li><li>[1.25](./build-files/multiqc/1.25/)</li><li>[1.26](./build-files/multiqc/1.26/)</li><li>[1.27.1](./build-files/multiqc/1.27.1/)</li><li>[1.28](./build-files/multiqc/1.28/)</li><li>[1.30](./build-files/multiqc/1.30/)</li><li>[1.31](./build-files/multiqc/1.31/)</li><li>[1.33](./build-files/multiqc/1.33/)</li><li>[1.34](./build-files/multiqc/1.34/)</li><li>[1.35](./build-files/multiqc/1.35/)</li></ul> </details> | https://github.com/MultiQC/MultiQC |
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| [Mummer](https://hub.docker.com/r/staphb/mummer) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/mummer)](https://hub.docker.com/r/staphb/mummer) | <details><summary>Click to see all versions</summary> <ul><li>[4.0.0](./build-files/mummer/4.0.0/)</li><li>[4.0.0 + RGDv2](./build-files/mummer/4.0.0-RGDv2/)</li><li>[4.0.0 + RGDv2 + gnuplot](./build-files/mummer/4.0.0-gnuplot/)</li><li>[4.0.1](./build-files/mummer/4.0.1/)</li></ul> </details> | https://github.com/mummer4/mummer |
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| [Mykrobe + Genotyphi + sonneityping](https://hub.docker.com/r/staphb/mykrobe) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/mykrobe)](https://hub.docker.com/r/staphb/mykrobe) | <details><summary> Click to see all versions </summary><ul><li>[0.11.0 (Mykrobe) & 1.9.1 (Genotyphi)](./build-files/mykrobe/0.11.0/) </li><li>[0.12.1 (Mykrobe) & 1.9.1 (Genotyphi) & 7d18a7c (sonneityping)](./build-files/mykrobe/0.12.1-sonneityping/) </li><li>[0.12.1 (Mykrobe) & 2.0 (Genotyphi) & v20210201 (sonneityping)](./build-files/mykrobe/0.12.1/) </li><li>[0.12.2 (Mykrobe) & 2.0 (Genotyphi) & v20210201 (sonneityping)](./build-files/mykrobe/0.12.2/)</li><li>[0.13.0](./build-files/mykrobe/0.13.0)</li><li>[0.13.0 (Mykrobe) & 2.1 (Genotyphi) & v20210201 (sonneityping)](./build-files/mykrobe/0.13.0-genotyphi-2.1/)</li></ul></details> | https://github.com/Mykrobe-tools/mykrobe <br/> https://github.com/typhoidgenomics/genotyphi <br/> https://github.com/katholt/sonneityping |
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| [myloasm](https://hub.docker.com/r/staphb/myloasm) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/myloasm)](https://hub.docker.com/r/staphb/myloasm) | <details><summary> Click to see all versions </summary><ul><li>[0.1.0](./build-files/myloasm/0.1.0/)</li><li>[0.2.0](./build-files/myloasm/0.2.0/)</li><li>[0.3.0](./build-files/myloasm/0.3.0/)</li><li>[0.5.1](./build-files/myloasm/0.5.1/)</li></ul></details> | https://github.com/bluenote-1577/myloasm |

‎build-files/multiqc/1.35/Dockerfile‎

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FROM ubuntu:noble AS app
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ARG MULTIQC_VER="1.35"
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# metadata
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LABEL base.image="ubuntu:noble"
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LABEL dockerfile.version="1"
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LABEL software="MultiQC"
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LABEL software.version="${MULTIQC_VER}"
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LABEL description="Aggregate bioinformatics results across many samples into a single report."
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LABEL website="https://github.com/MultiQC/MultiQC"
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LABEL license="https://github.com/MultiQC/MultiQC/blob/main/LICENSE"
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LABEL maintainer="Erin Young"
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LABEL maintainer.email="eriny@utah.gov"
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RUN apt-get update && apt-get install --no-install-recommends -y \
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python3-pip && \
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apt-get clean && apt-get autoclean && rm -rf /var/lib/apt/lists/*
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# install multiqc
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RUN pip3 install --no-cache-dir --break-system-packages multiqc==${MULTIQC_VER}
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ENV LC_ALL='C.UTF-8' \
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LANG='C.UTF-8'
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CMD ["multiqc", "--help"]
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RUN mkdir /data
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WORKDIR /data
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# testing layer starts here
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FROM app AS test
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# getting git
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RUN apt-get update && apt-get install -y git
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# to ensure multiqc is in PATH
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RUN multiqc --version && multiqc --help
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# set working directory so that all test inputs & outputs are kept in /test
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RUN mkdir /test
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WORKDIR /test
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# getting multiqc test data
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RUN git clone https://github.com/ewels/MultiQC_TestData && \
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multiqc . && \
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ls multiqc_report.html
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RUN pip list

‎build-files/multiqc/1.35/README.md‎

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# MultiQC container
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Main tool : [MultiQC](https://multiqc.info/)
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Aggregate results from bioinformatics analyses across many samples into a single report.
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Full documentation: [Docs] (https://multiqc.info/docs/)
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Notes: Starting with version 1.27, multiqc can use ai to assist with summaries. More information on how to set this up and use it can be found at https://docs.seqera.io/multiqc/ai.
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<details>
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<summary>
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Additional tools installed via pip:
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</summary>
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```
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Package Version
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------------------------- -----------
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annotated-types 0.7.0
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attrs 26.1.0
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boto3 1.43.36
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botocore 1.43.36
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certifi 2026.6.17
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charset-normalizer 3.4.7
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click 8.4.2
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coloredlogs 15.0.1
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colormath2 3.0.3
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humanfriendly 10.0
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humanize 4.15.0
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idna 3.18
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importlib_metadata 9.0.0
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Jinja2 3.1.6
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jmespath 1.1.0
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jsonschema 4.26.0
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jsonschema-specifications 2025.9.1
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kaleido 0.2.1
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Markdown 3.10.2
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markdown-it-py 4.2.0
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MarkupSafe 3.0.3
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mdurl 0.1.2
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multiqc 1.35
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narwhals 2.22.1
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natsort 8.4.0
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networkx 3.6.1
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numpy 2.5.0
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packaging 26.2
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pillow 12.2.0
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pip 24.0
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plotly 6.8.0
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polars 1.42.0
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polars-runtime-32 1.42.0
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polars-runtime-compat 1.42.0
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pyarrow 24.0.0
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pydantic 2.13.4
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pydantic_core 2.46.4
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Pygments 2.20.0
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python-dateutil 2.9.0.post0
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python-dotenv 1.2.2
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PyYAML 6.0.3
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referencing 0.37.0
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regex 2026.5.9
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requests 2.34.2
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rich 15.0.0
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rich-click 1.9.8
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rpds-py 2026.5.1
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s3transfer 0.19.0
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setuptools 68.1.2
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six 1.17.0
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spectra 0.1.0
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tiktoken 0.13.0
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tqdm 4.68.3
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typeguard 4.5.2
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typing_extensions 4.15.0
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typing-inspection 0.4.2
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urllib3 2.7.0
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wheel 0.42.0
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zipp 4.1.0
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```
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</details>
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# Example Usage
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```
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multiqc -f --cl_config "prokka_fn_snames: True" .
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```

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