multiqc not recognising mgikit report files

[ajeffs]

Hi,

Thanks for mgikit, really useful tool!

I've installed mgikit-multiqc without any issue as far as I can tell (substituting python3 for python because of a "Command 'python' not found error with 'python setup.py install') :

sudo python3 setup.py install
running install
/usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
!!

    ********************************************************************************
    Please avoid running ``setup.py`` directly.
    Instead, use pypa/build, pypa/installer or other
    standards-based tools.

    See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
    ********************************************************************************

!!
self.initialize_options()
/usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: EasyInstallDeprecationWarning: easy_install command is deprecated.
!!

    ********************************************************************************
    Please avoid running ``setup.py`` and ``easy_install``.
    Instead, use pypa/build, pypa/installer or other
    standards-based tools.

    See https://github.com/pypa/setuptools/issues/917 for details.
    ********************************************************************************

!!
self.initialize_options()
running bdist_egg
running egg_info
writing multiqc_mgikit_plugin.egg-info/PKG-INFO
writing dependency_links to multiqc_mgikit_plugin.egg-info/dependency_links.txt
writing entry points to multiqc_mgikit_plugin.egg-info/entry_points.txt
writing requirements to multiqc_mgikit_plugin.egg-info/requires.txt
writing top-level names to multiqc_mgikit_plugin.egg-info/top_level.txt
reading manifest file 'multiqc_mgikit_plugin.egg-info/SOURCES.txt'
adding license file 'LICENSE'
writing manifest file 'multiqc_mgikit_plugin.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/mgikit
copying build/lib/mgikit/init.py -> build/bdist.linux-x86_64/egg/mgikit
creating build/bdist.linux-x86_64/egg/mgikit/modules
copying build/lib/mgikit/modules/init.py -> build/bdist.linux-x86_64/egg/mgikit/modules
creating build/bdist.linux-x86_64/egg/mgikit/modules/mgikit
copying build/lib/mgikit/modules/mgikit/init.py -> build/bdist.linux-x86_64/egg/mgikit/modules/mgikit
copying build/lib/mgikit/modules/mgikit/mgikit.py -> build/bdist.linux-x86_64/egg/mgikit/modules/mgikit
copying build/lib/mgikit/cli.py -> build/bdist.linux-x86_64/egg/mgikit
copying build/lib/mgikit/custom_code.py -> build/bdist.linux-x86_64/egg/mgikit
byte-compiling build/bdist.linux-x86_64/egg/mgikit/init.py to init.cpython-312.pyc
byte-compiling build/bdist.linux-x86_64/egg/mgikit/modules/init.py to init.cpython-312.pyc
byte-compiling build/bdist.linux-x86_64/egg/mgikit/modules/mgikit/init.py to init.cpython-312.pyc
byte-compiling build/bdist.linux-x86_64/egg/mgikit/modules/mgikit/mgikit.py to mgikit.cpython-312.pyc
byte-compiling build/bdist.linux-x86_64/egg/mgikit/cli.py to cli.cpython-312.pyc
byte-compiling build/bdist.linux-x86_64/egg/mgikit/custom_code.py to custom_code.cpython-312.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying multiqc_mgikit_plugin.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying multiqc_mgikit_plugin.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying multiqc_mgikit_plugin.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying multiqc_mgikit_plugin.egg-info/entry_points.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying multiqc_mgikit_plugin.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying multiqc_mgikit_plugin.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
zip_safe flag not set; analyzing archive contents...
creating 'dist/multiqc_mgikit_plugin-0.3-py3.12.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing multiqc_mgikit_plugin-0.3-py3.12.egg
Removing /usr/local/lib/python3.12/dist-packages/multiqc_mgikit_plugin-0.3-py3.12.egg
Copying multiqc_mgikit_plugin-0.3-py3.12.egg to /usr/local/lib/python3.12/dist-packages
Adding multiqc-mgikit-plugin 0.3 to easy-install.pth file

Installed /usr/local/lib/python3.12/dist-packages/multiqc_mgikit_plugin-0.3-py3.12.egg
Processing dependencies for multiqc-mgikit-plugin==0.3
Searching for rich-click
Reading https://pypi.org/simple/rich-click/
Downloading https://files.pythonhosted.org/packages/c6/ea/5a0c5a8e6532e971983d1b0fc99268eb66a10f489da35d9022ce01044191/rich_click-1.8.3-py3-none-any.whl#sha256=636d9c040d31c5eee242201b5bf4f2d358bfae4db14bb22ec1cafa717cfd02cd
Best match: rich-click 1.8.3
Processing rich_click-1.8.3-py3-none-any.whl
Installing rich_click-1.8.3-py3-none-any.whl to /usr/local/lib/python3.12/dist-packages
Adding rich-click 1.8.3 to easy-install.pth file
Installing rich-click script to /usr/local/bin

Installed /usr/local/lib/python3.12/dist-packages/rich_click-1.8.3-py3.12.egg
Searching for pydantic>=2.7.0
Reading https://pypi.org/simple/pydantic/
Downloading https://files.pythonhosted.org/packages/df/e4/ba44652d562cbf0bf320e0f3810206149c8a4e99cdbf66da82e97ab53a15/pydantic-2.9.2-py3-none-any.whl#sha256=f048cec7b26778210e28a0459867920654d48e5e62db0958433636cde4254f12
Best match: pydantic 2.9.2
Processing pydantic-2.9.2-py3-none-any.whl
Installing pydantic-2.9.2-py3-none-any.whl to /usr/local/lib/python3.12/dist-packages
Adding pydantic 2.9.2 to easy-install.pth file
detected new path './rich_click-1.8.3-py3.12.egg'

Installed /usr/local/lib/python3.12/dist-packages/pydantic-2.9.2-py3.12.egg
Searching for plotly>=5.18
Reading https://pypi.org/simple/plotly/
Downloading https://files.pythonhosted.org/packages/e5/ae/580600f441f6fc05218bd6c9d5794f4aef072a7d9093b291f1c50a9db8bc/plotly-5.24.1-py3-none-any.whl#sha256=f67073a1e637eb0dc3e46324d9d51e2fe76e9727c892dde64ddf1e1b51f29089
Best match: plotly 5.24.1
Processing plotly-5.24.1-py3-none-any.whl
Installing plotly-5.24.1-py3-none-any.whl to /usr/local/lib/python3.12/dist-packages
Adding plotly 5.24.1 to easy-install.pth file
detected new path './pydantic-2.9.2-py3.12.egg'

Installed /usr/local/lib/python3.12/dist-packages/plotly-5.24.1-py3.12.egg
Searching for markdown
Reading https://pypi.org/simple/markdown/
Downloading https://files.pythonhosted.org/packages/3f/08/83871f3c50fc983b88547c196d11cf8c3340e37c32d2e9d6152abe2c61f7/Markdown-3.7-py3-none-any.whl#sha256=7eb6df5690b81a1d7942992c97fad2938e956e79df20cbc6186e9c3a77b1c803
Best match: Markdown 3.7
Processing Markdown-3.7-py3-none-any.whl
Installing Markdown-3.7-py3-none-any.whl to /usr/local/lib/python3.12/dist-packages
Adding Markdown 3.7 to easy-install.pth file
detected new path './plotly-5.24.1-py3.12.egg'
Installing markdown_py script to /usr/local/bin

Installed /usr/local/lib/python3.12/dist-packages/Markdown-3.7-py3.12.egg
Searching for kaleido
Reading https://pypi.org/simple/kaleido/
Downloading https://files.pythonhosted.org/packages/ae/b3/a0f0f4faac229b0011d8c4a7ee6da7c2dca0b6fd08039c95920846f23ca4/kaleido-0.2.1-py2.py3-none-manylinux1_x86_64.whl#sha256=aa21cf1bf1c78f8fa50a9f7d45e1003c387bd3d6fe0a767cfbbf344b95bdc3a8
Best match: kaleido 0.2.1
Processing kaleido-0.2.1-py2.py3-none-manylinux1_x86_64.whl
Installing kaleido-0.2.1-py2.py3-none-manylinux1_x86_64.whl to /usr/local/lib/python3.12/dist-packages
Adding kaleido 0.2.1 to easy-install.pth file
detected new path './Markdown-3.7-py3.12.egg'

Installed /usr/local/lib/python3.12/dist-packages/kaleido-0.2.1-py3.12-linux-x86_64.egg
Searching for humanize
Reading https://pypi.org/simple/humanize/
Downloading https://files.pythonhosted.org/packages/92/75/4bc3e242ad13f2e6c12e0b0401ab2c5e5c6f0d7da37ec69bc808e24e0ccb/humanize-4.11.0-py3-none-any.whl#sha256=b53caaec8532bcb2fff70c8826f904c35943f8cecaca29d272d9df38092736c0
Best match: humanize 4.11.0
Processing humanize-4.11.0-py3-none-any.whl
Installing humanize-4.11.0-py3-none-any.whl to /usr/local/lib/python3.12/dist-packages
Adding humanize 4.11.0 to easy-install.pth file
detected new path './kaleido-0.2.1-py3.12-linux-x86_64.egg'

Installed /usr/local/lib/python3.12/dist-packages/humanize-4.11.0-py3.12.egg
Searching for coloredlogs
Reading https://pypi.org/simple/coloredlogs/
Downloading https://files.pythonhosted.org/packages/a7/06/3d6badcf13db419e25b07041d9c7b4a2c331d3f4e7134445ec5df57714cd/coloredlogs-15.0.1-py2.py3-none-any.whl#sha256=612ee75c546f53e92e70049c9dbfcc18c935a2b9a53b66085ce9ef6a6e5c0934
Best match: coloredlogs 15.0.1
Processing coloredlogs-15.0.1-py2.py3-none-any.whl
Installing coloredlogs-15.0.1-py2.py3-none-any.whl to /usr/local/lib/python3.12/dist-packages
Adding coloredlogs 15.0.1 to easy-install.pth file
detected new path './humanize-4.11.0-py3.12.egg'
Installing coloredlogs script to /usr/local/bin

Installed /usr/local/lib/python3.12/dist-packages/coloredlogs-15.0.1-py3.12.egg
Searching for typing-extensions>=4.10.0
Reading https://pypi.org/simple/typing-extensions/
Downloading https://files.pythonhosted.org/packages/26/9f/ad63fc0248c5379346306f8668cda6e2e2e9c95e01216d2b8ffd9ff037d0/typing_extensions-4.12.2-py3-none-any.whl#sha256=04e5ca0351e0f3f85c6853954072df659d0d13fac324d0072316b67d7794700d
Best match: typing-extensions 4.12.2
Processing typing_extensions-4.12.2-py3-none-any.whl
Installing typing_extensions-4.12.2-py3-none-any.whl to /usr/local/lib/python3.12/dist-packages
Adding typing-extensions 4.12.2 to easy-install.pth file
detected new path './coloredlogs-15.0.1-py3.12.egg'

Installed /usr/local/lib/python3.12/dist-packages/typing_extensions-4.12.2-py3.12.egg
Searching for pydantic-core==2.23.4
Reading https://pypi.org/simple/pydantic-core/
Downloading https://files.pythonhosted.org/packages/06/c8/7d4b708f8d05a5cbfda3243aad468052c6e99de7d0937c9146c24d9f12e9/pydantic_core-2.23.4-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#sha256=128585782e5bfa515c590ccee4b727fb76925dd04a98864182b22e89a4e6ed36
Best match: pydantic-core 2.23.4
Processing pydantic_core-2.23.4-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Installing pydantic_core-2.23.4-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl to /usr/local/lib/python3.12/dist-packages
Adding pydantic-core 2.23.4 to easy-install.pth file
detected new path './typing_extensions-4.12.2-py3.12.egg'

Installed /usr/local/lib/python3.12/dist-packages/pydantic_core-2.23.4-py3.12-linux-x86_64.egg
Searching for annotated-types>=0.6.0
Reading https://pypi.org/simple/annotated-types/
Downloading https://files.pythonhosted.org/packages/78/b6/6307fbef88d9b5ee7421e68d78a9f162e0da4900bc5f5793f6d3d0e34fb8/annotated_types-0.7.0-py3-none-any.whl#sha256=1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53
Best match: annotated-types 0.7.0
Processing annotated_types-0.7.0-py3-none-any.whl
Installing annotated_types-0.7.0-py3-none-any.whl to /usr/local/lib/python3.12/dist-packages
Adding annotated-types 0.7.0 to easy-install.pth file
detected new path './pydantic_core-2.23.4-py3.12-linux-x86_64.egg'

Installed /usr/local/lib/python3.12/dist-packages/annotated_types-0.7.0-py3.12.egg
Searching for tenacity>=6.2.0
Reading https://pypi.org/simple/tenacity/
Downloading https://files.pythonhosted.org/packages/b6/cb/b86984bed139586d01532a587464b5805f12e397594f19f931c4c2fbfa61/tenacity-9.0.0-py3-none-any.whl#sha256=93de0c98785b27fcf659856aa9f54bfbd399e29969b0621bc7f762bd441b4539
Best match: tenacity 9.0.0
Processing tenacity-9.0.0-py3-none-any.whl
Installing tenacity-9.0.0-py3-none-any.whl to /usr/local/lib/python3.12/dist-packages
Adding tenacity 9.0.0 to easy-install.pth file
detected new path './annotated_types-0.7.0-py3.12.egg'

Installed /usr/local/lib/python3.12/dist-packages/tenacity-9.0.0-py3.12.egg
Searching for humanfriendly>=9.1
Reading https://pypi.org/simple/humanfriendly/
Downloading https://files.pythonhosted.org/packages/f0/0f/310fb31e39e2d734ccaa2c0fb981ee41f7bd5056ce9bc29b2248bd569169/humanfriendly-10.0-py2.py3-none-any.whl#sha256=1697e1a8a8f550fd43c2865cd84542fc175a61dcb779b6fee18cf6b6ccba1477
Best match: humanfriendly 10.0
Processing humanfriendly-10.0-py2.py3-none-any.whl
Installing humanfriendly-10.0-py2.py3-none-any.whl to /usr/local/lib/python3.12/dist-packages
Adding humanfriendly 10.0 to easy-install.pth file
detected new path './tenacity-9.0.0-py3.12.egg'
Installing humanfriendly script to /usr/local/bin

Installed /usr/local/lib/python3.12/dist-packages/humanfriendly-10.0-py3.12.egg
Searching for multiqc==1.25.1
Best match: multiqc 1.25.1
Processing multiqc-1.25.1-py3.12.egg
Adding multiqc 1.25.1 to easy-install.pth file
detected new path './humanfriendly-10.0-py3.12.egg'
Installing multiqc script to /usr/local/bin

Using /usr/local/lib/python3.12/dist-packages/multiqc-1.25.1-py3.12.egg
Searching for typeguard==4.3.0
Best match: typeguard 4.3.0
Processing typeguard-4.3.0-py3.12.egg
Adding typeguard 4.3.0 to easy-install.pth file

Using /usr/local/lib/python3.12/dist-packages/typeguard-4.3.0-py3.12.egg
Searching for tqdm==4.66.5
Best match: tqdm 4.66.5
Processing tqdm-4.66.5-py3.12.egg
Adding tqdm 4.66.5 to easy-install.pth file
Installing tqdm script to /usr/local/bin

Using /usr/local/lib/python3.12/dist-packages/tqdm-4.66.5-py3.12.egg
Searching for spectra==0.0.11
Best match: spectra 0.0.11
Adding spectra 0.0.11 to easy-install.pth file

Using /usr/lib/python3/dist-packages
Searching for rich==13.7.1
Best match: rich 13.7.1
Adding rich 13.7.1 to easy-install.pth file

Using /usr/lib/python3/dist-packages
Searching for requests==2.31.0
Best match: requests 2.31.0
Adding requests 2.31.0 to easy-install.pth file

Using /usr/lib/python3/dist-packages
Searching for PyYAML==6.0.1
Best match: PyYAML 6.0.1
Adding PyYAML 6.0.1 to easy-install.pth file

Using /usr/lib/python3/dist-packages
Searching for packaging==24.0
Best match: packaging 24.0
Adding packaging 24.0 to easy-install.pth file

Using /usr/lib/python3/dist-packages
Searching for numpy==1.26.4
Best match: numpy 1.26.4
Adding numpy 1.26.4 to easy-install.pth file
Installing f2py script to /usr/local/bin
Installing f2py3 script to /usr/local/bin
Installing f2py3.12 script to /usr/local/bin

Using /usr/lib/python3/dist-packages
Searching for Jinja2==3.1.2
Best match: Jinja2 3.1.2
Adding Jinja2 3.1.2 to easy-install.pth file

Using /usr/lib/python3/dist-packages
Searching for importlib-metadata==4.12.0
Best match: importlib-metadata 4.12.0
Adding importlib-metadata 4.12.0 to easy-install.pth file

Using /usr/lib/python3/dist-packages
Searching for click==8.1.6
Best match: click 8.1.6
Adding click 8.1.6 to easy-install.pth file

Using /usr/lib/python3/dist-packages
Searching for pillow==10.2.0
Best match: pillow 10.2.0
Adding pillow 10.2.0 to easy-install.pth file

Using /usr/lib/python3/dist-packages
Searching for pygments==2.17.2
Best match: pygments 2.17.2
Adding pygments 2.17.2 to easy-install.pth file
Installing pygmentize script to /usr/local/bin

Using /usr/lib/python3/dist-packages
Searching for markdown-it-py==3.0.0
Best match: markdown-it-py 3.0.0
Adding markdown-it-py 3.0.0 to easy-install.pth file
Installing markdown-it script to /usr/local/bin

Using /usr/lib/python3/dist-packages
Searching for zipp==1.0.0
Best match: zipp 1.0.0
Adding zipp 1.0.0 to easy-install.pth file

Using /usr/lib/python3/dist-packages
Searching for mdurl==0.1.2
Best match: mdurl 0.1.2
Adding mdurl 0.1.2 to easy-install.pth file

Using /usr/lib/python3/dist-packages
Searching for more-itertools==10.2.0
Best match: more-itertools 10.2.0
Adding more-itertools 10.2.0 to easy-install.pth file

Using /usr/lib/python3/dist-packages
Finished processing dependencies for multiqc-mgikit-plugin==0.3

'multiqc -h' shows mgikit-multiqc options:

Options ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --clean-up/--no-clean-up    Remove the temporary directory and log file after finishing                                                                                               │
│ --no-version-check          Disable checking the latest MultiQC version on the server                                                                                                 │
│ --brief-report              generate a brief version of the report. This ignores the reports for cluster per sample per lane.                                                         │
│ --decimal-positions         The number of decimal positions to be used with the values in teh tables of mgikit. 2 decimal positions is the default option. (INTEGER)                  │
│ --disable-mgikit-plugin     Disable the mgikit MultiQC plugin on this run                                                                                                             │
│ --keep-core-samples         Ignore undetermined and ambiguous cases in the report.                                                                                                    │
│ --undetermined-barcode      Set the number of undetermined barcodes to be presented in the report. (INTEGER)   

So I understand that to mean that the mgikit-multiqc plugin is installed and seen by multiqc.

However, when running multiqc none of the mgikit report files are recognised as valid results:

multiqc mgikit-examples/test/

/// MultiQC 🔍 v1.25.1

       file_search | Search path: /home/ajeffs/mgikit-multiqc/mgikit-examples/test
         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 5/5  
           multiqc | No analysis results found. Cleaning up…

Any feedback on what might me happening here, and what I might have done wrong, would be very much appreciated!

All the best,

Aaron.

[ajeffs]

Adding verbose multiqc output:

multiqc -v mgikit-examples/test/

/// MultiQC 🔍 v1.25.1

[2024-10-09 15:12:16] multiqc.core.tmp_dir                               [DEBUG  ]  Using new temporary directory: /tmp/tmp4ihj0ptn
[2024-10-09 15:12:16] root                                               [DEBUG  ]  Logging to file: /tmp/tmp4ihj0ptn/multiqc.log
[2024-10-09 15:12:16] multiqc.core.update_config                         [DEBUG  ]  This is MultiQC v1.25.1
[2024-10-09 15:12:16] multiqc.core.update_config                         [DEBUG  ]  Running Python 3.12.3 (main, Sep 11 2024, 14:17:37) [GCC 13.2.0]
[2024-10-09 15:12:16] urllib3.connectionpool                             [DEBUG  ]  Starting new HTTPS connection (1): api.multiqc.info:443
[2024-10-09 15:12:17] urllib3.connectionpool                             [DEBUG  ]  https://api.multiqc.info:443 "GET /version?version_multiqc=1.25.1&version_python=3.12.3&operating_system=Linux&is_docker=False&is_singularity=False&is_conda=False&is_ci=False&is_notebook=False HTTP/1.1" 200 182
[2024-10-09 15:12:17] multiqc.core.version_check                         [DEBUG  ]  Latest MultiQC version is v1.25.1, released 2024-10-01
[2024-10-09 15:12:17] multiqc.multiqc                                    [DEBUG  ]  Working dir : /home/ajeffs/mgikit-multiqc
[2024-10-09 15:12:17] multiqc.multiqc                                    [DEBUG  ]  Template    : default
[2024-10-09 15:12:17] multiqc.multiqc                                    [DEBUG  ]  Command used: /home/ajeffs/.local/bin/multiqc -v mgikit-examples/test/
[2024-10-09 15:12:17] multiqc.core.file_search                           [INFO   ]  Search path: /home/ajeffs/mgikit-multiqc/mgikit-examples/test
[2024-10-09 15:12:17] multiqc.core.file_search                           [DEBUG  ]  Analysing modules: mgikit, custom_content, ccs, ngsderive, purple, conpair, isoseq, lima, peddy, somalier, methylqa, mosdepth, phantompeakqualtools, qualimap, bamdst, preseq, hifiasm, quast, qorts, rna_seqc, rockhopper, rsem, rseqc, busco, bustools, goleft_indexcov, gffcompare, disambiguate, supernova, deeptools, sargasso, verifybamid, mirtrace, happy, mirtop, glimpse, gopeaks, homer, hops, macs2, theta2, snpeff, gatk, htseq, bcftools, featurecounts, fgbio, dragen, dragen_fastqc, dedup, pbmarkdup, damageprofiler, mapdamage, biobambam2, jcvi, mtnucratio, picard, vep, bakta, prokka, qc3C, nanoq, nanostat, samblaster, samtools, bamtools, sambamba, ngsbits, pairtools, sexdeterrmine, seqera_cli, eigenstratdatabasetools, jellyfish, vcftools, longranger, stacks, varscan2, snippy, umicollapse, umitools, truvari, megahit, ganon, bbmap, bismark, biscuit, diamond, hicexplorer, hicup, hicpro, salmon, kallisto, slamdunk, star, hisat2, tophat, bowtie2, bowtie1, hostile, cellranger, snpsplit, odgi, vg, pangolin, nextclade, freyja, humid, kat, leehom, librarian, nonpareil, adapterremoval, bbduk, clipandmerge, cutadapt, flexbar, sourmash, kaiju, kraken, malt, motus, trimmomatic, sickle, skewer, sortmerna, biobloomtools, fastq_screen, afterqc, fastp, fastqc, sequali, filtlong, prinseqplusplus, pychopper, porechop, pycoqc, minionqc, anglerfish, multivcfanalyzer, clusterflow, checkqc, bcl2fastq, bclconvert, interop, ivar, flash, seqyclean, optitype, whatshap, spaceranger, xenome, xengsort, metaphlan, seqwho, software_versions
         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 5/5  
[2024-10-09 15:12:17] multiqc.report                                     [DEBUG  ]  Summary of files that were skipped by the search: |skipped_no_match: 3|, |skipped_module_specific_max_filesize: 2|
[2024-10-09 15:12:17] multiqc.core.exec_modules                          [DEBUG  ]  Running module: custom_content
[2024-10-09 15:12:17] multiqc.core.exec_modules                          [DEBUG  ]  No samples found: custom_content
[2024-10-09 15:12:17] multiqc.core.exec_modules                          [DEBUG  ]  Running module: htseq
[2024-10-09 15:12:17] multiqc.core.exec_modules                          [DEBUG  ]  No samples found: htseq
[2024-10-09 15:12:17] multiqc.core.software_versions                     [DEBUG  ]  Reading software versions from config.software_versions
[2024-10-09 15:12:17] multiqc.multiqc                                    [WARNING]  No analysis results found. Cleaning up…