adding multiqc 1.22.2

[erinyoung]

There's a new version of multiqc (https://github.com/MultiQC/MultiQC/releases/tag/v1.21)!

There are now box plots and some new supported tools.

I copied the Dockerfile from verison 1.19 and updated the software version ARG.

Pull Request (PR) checklist:

• Include a description of what is in this pull request in this message.
• The dockerfile successfully builds to a test target for the user creating the PR. (i.e. docker build --tag samtools:1.15test --target test docker-builds/samtools/1.15 )
• Directory structure as name of the tool in lower case with special characters removed with a subdirectory of the version number (i.e. spades/3.12.0/Dockerfile)
  • (optional) All test files are located in same directory as the Dockerfile (i.e. shigatyper/2.0.1/test.sh)
• Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. spades/3.12.0/README.md)
  • If this README is longer than 30 lines, there is an explanation as to why more detail was needed
• Dockerfile includes the recommended LABELS
• Main README.md has been updated to include the tool and/or version of the dockerfile(s) in this PR
• Program_Licenses.md contains the tool(s) used in this PR and has been updated for any missing

[erinyoung]

Error should be fixed in next MultiQC release

[erinyoung]

There are some warnings about the table property, but appears to work as expected. I think this is ready for review.

[erinyoung]

I guess there was some nextflow issues with 1.22, so they made some updates and released 1.22.1

[erinyoung]

@kevinlibuit , do you have time to review this?

[Kincekara]

@erinyoung sorry for my excess comments! To make your life easier I am adding a dockerfile below.
--pdf does not give an error but also does not work even if pandoc and textlive-xetex are installed. I suggest removing those packages since they add an extra ~500MB to uncompressed images. Our image is 616 MB on dockerhub while the developer's is 174MB. If it works and you want to keep them, please add them back.

FROM ubuntu:jammy as app

ARG MULTIQC_VER="1.22.2"

LABEL base.image="ubuntu:jammy"
LABEL dockerfile.version="1"
LABEL software="MultiQC"
LABEL software.version="${MULTIQC_VER}"
LABEL description="Aggregate bioinformatics results across many samples into a single report."
LABEL website="https://github.com/MultiQC/MultiQC"
LABEL license="https://github.com/MultiQC/MultiQC/blob/main/LICENSE"
LABEL maintainer="Erin Young"
LABEL maintainer.email="eriny@utah.gov"

RUN apt-get update && apt-get install --no-install-recommends -y \
    python3-pip \
    locales &&\
    locale-gen en_US.UTF-8 &&\
    apt-get clean && apt-get autoclean && rm -rf /var/lib/apt/lists/*

RUN pip install --no-cache-dir "multiqc==${MULTIQC_VER}"

ENV LC_ALL=C.UTF-8 \
    LANG=en_US.UTF-8

CMD multiqc --help

WORKDIR /data

## Test ##
FROM app as test

RUN apt-get update && apt-get install --no-install-recommends -y git

RUN git clone https://github.com/MultiQC/test-data && \
    multiqc ./test-data/data && \
    ls multiqc_report.html 

[erinyoung]

I'm okay with giving up pandoc.

I also like your suggestion of not installing git or wget. That will also help reduce size.

[erinyoung]

It looks like it runs okay

#15 9.784 /// MultiQC 🔍 v1.22.2
#15 9.784 
#15 10.20        file_search | Search path: /test
#15 15.77 
#15 15.80     custom_content | No data found in test_html_mqc.yaml
#15 15.80     custom_content | Test-Mire2: Found 1 sample (image)
#15 15.80     custom_content | some_science: Found 1 sample (image)
#15 15.80     custom_content | dupRadar_plot: Found 1 sample (image)
#15 15.83     custom_content | heatmap_example: Found 4 samples (heatmap)
#15 15.83     custom_content | sample_4: Found 1 samples (linegraph)
#15 15.83     custom_content | sample_3: Found 1 samples (linegraph)
#15 15.83     custom_content | sample_1: Found 1 samples (linegraph)
#15 15.84     custom_content | sample_2: Found 1 samples (linegraph)
#15 15.84     custom_content | linegraph_multiple_samples: Found 1 samples (linegraph)
#15 15.85     custom_content | issue_1091: Found 1 samples (table)
#15 15.86     custom_content | no_header: Found 1 samples (bargraph)
#15 15.86     custom_content | table_data: Found 1 samples (table)
#15 15.87     custom_content | big_heatmap: Found 32 samples (heatmap)
#15 15.87     custom_content | my_test: Found 1 sample (html)
#15 15.87     custom_content | bargraph_multiple_samples: Found 1 samples (bargraph)
#15 15.88     custom_content | mqc_pca2: Found 3 samples (scatter)
#15 15.88     custom_content | xhet_section: Found 1 samples (scatter)
#15 15.89     custom_content | test_table: Found 1 samples (table)
#15 15.89     custom_content | custom_bargraph_tsv: Found 1 samples (bargraph)
#15 15.90     custom_content | ivar_variants: Found 1 samples (bargraph)
#15 15.90     custom_content | mqc_pca: Found 1 samples (scatter)
#15 21.95           porechop | Found 2 reports
#15 22.07             pycoqc | Found 3 reports
#15 22.10           minionqc | Found 2 reports
#15 22.12         anglerfish | Found 1 reports
#15 22.15        clusterflow | Found 4 pipelines
#15 22.16            checkqc | Found 1 run and 6 samples
#15 22.26         bclconvert | Found RunInfo.xml file in MultiQC_TestData/data/modules/bclconvert/3.9.3/merged/Reports but no Demux Stats file, skipping
#15 22.29         bclconvert | Found multiple sequencer runs
#15 22.29         bclconvert | 14 lanes and 237 samples found
#15 22.33            interop | Found 3 reports
#15 22.36               ivar | Found 3 reports
#15 22.37              flash | Found 5 log reports
#15 22.38              flash | Found 4 histogram reports
#15 22.38          seqyclean | Found 6 logs
#15 22.40           optitype | Found 1 reports
#15 22.41           whatshap | Could not find the 'ALL' chromosome for GM24385_0_1x_full_opt_trunc. Make sure that the input is not truncated. MultiQC will summarize information for all available chromosomes instead.
#15 22.64        spaceranger | Found 7 Space Ranger count reports
#15 22.64             xenome | Found 3 reports
#15 22.66           xengsort | Found 1 reports
#15 22.68          metaphlan | Found 1 reports
#15 22.69             seqwho | Found 1 reports
#15 52.71              table | Tried to sort by column 'libraries_affected', but column was not found. Available columns: []
#15 62.34      write_results | Data        : multiqc_data
#15 64.08      write_results | Report      : multiqc_report.html
#15 64.08            multiqc | MultiQC com

[Kincekara]

Thank you for the update! I made a few minor changes and merged it.
Deploy link: https://github.com/StaPH-B/docker-builds/actions/runs/9500851856