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change the or to and

the line:

When calculating an eigenvector you may change its sign and the solution will also be a valid one.

So any PCA axis can be reversed and the solution will be valid.

Nevertheless, you may wish to impose a positive correlation of a PCA axis with one of the original variables in the dataset, inverting the axis if needed.

I suggest adding the entities path oin your config so it can find files :

The rule that fails is rule guppyplex, which looks for an input in the form of {FASTQ_PATH}/{{barcode}}.

Looks like the wildcard {barcode} is filled with barcode49/barcode49.consensus.fasta, which happened because of two reasons I think:

First (and most important): The workflow does not find a better way to produce the final output. In rule catFasta, you give an input file which is never described as an output in your workflow. The rule minion has the directory as an output, but not the file, and it is not perfectly clear for the workflow where to produce this input file.

It therefore infers that the {barcode} wildcard somehow has to contain this .consensus.fasta that it has never seen before. This wildcard is then handed over to the top, where the workflow crashes since it cannot find a matching input file.

Second: This initialisation of the wildcard with sth. you don't want is only possible since you did not constrain the wildcard properly. You can for example forbid the wildcard to contain a . (see wildcard_constraints here)

However, the main problem is that catFasta does not find the desired input. I'd suggest changing the output of minion to "nanopolish/{barcode}/{barcode}.consensus.fasta", since the you already take the OUTDIR from the params, that should not hurt your rule here.

Edit: Dummy test example:

Change your function to -

I think you want conditional aggregation here:

I think I got the problem. First of all below is the way by which we can reproduce the error & the way you have proceed :

As I understand it, coverage is about reporting how much of your codebase is tested, not which tests to run. What you're doing is excluding things from a report, not stopping the data for the report being created.

What you should do is skip tests if you know they're going to fail (due to external configuration). Fortunately pytest provides for this with the skipif decorator.

I would create a function in tests/conftest.py which skips tests if the VPN is active. Something like:

This is easily done, since you can specify any function. So try