MultiQC: Added module tests back to test failure

[apeltzer]

Attempt at fixing MQC 1.13a0 with proper module testing. Not sure what went wrong the last time though :-(

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[ewels]

This is to fix the error seen here: nf-core/modules#1814 (review) which also seems to be the error happening in the BioConda CI tests:

$ docker run -it quay.io/biocontainers/multiqc:1.13a--pyhdfd78af_0
# multiqc
Traceback (most recent call last):
  File "/usr/local/bin/multiqc", line 10, in <module>
    sys.exit(multiqc())
TypeError: 'module' object is not callable

This bin/multiqc script is auto-generated by Conda during installation and doesn't come from the code base. It sounds to be like some kind of namespace error.

Note that this has been working for people doing pip installs directly from GitHub, as far as I know. So I think it's Conda-specific.

[ewels]

This diff shows what has changed since the last Bioconda release for v1.12: MultiQC/MultiQC@v1.12...master

One bit that catches my eye is a change in the function call in setup.py:

    entry_points={
        "console_scripts": [
-           "multiqc=multiqc.__main__:multiqc",
+           "multiqc=multiqc.__main__:run_multiqc",
        ],

Seems suspicious, but I'm not sure why that would break anything. I guess that this is the road that we need to go down to figure out and fix this error though.. 🤔

[apeltzer]

Just added that to the PR :-)

[apeltzer]

@BiocondaBot please add label

[apeltzer]

Yeah was the missing entry point in the meta.yaml that was updated in between 1.12 --> 1.13.

[ewels]

My bad, should have spotted this the first time around sorry.

[apeltzer]

My bad, should have spotted this the first time around sorry.

Our bad ;-)

[apeltzer]

@BiocondaBot please merge

[BiocondaBot]

I will attempt to upload artifacts and merge this PR. This may take some time, please have patience.