canvas/germline: Added tests and missing inputs, some cleanup

[Schmytzi]

• Added missing inputs and tests.
• Replaced genomedir input with separate kmer_fasta and genomesize inputs
• Removed automatic selection of ploidy VCF based on sex, now responsibility of the caller
• Removed dependency on external python script
• Replaced file operations on inputs with stageAs
• Added check that at least one SNV VCF is supplied
• Removed automatic filtering of REF calls, now responsibility of the caller
• Replaced hard-coded version with call to Canvas --version
• Skipping CI tests because of hard-coded request for 8 CPUs and 25 GB of RAM

Requires nf-core/test-datasets#2188 to be merged first.

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[maxulysse]

I don't like that no tests at all are run for this module

[erikrikarddaniel]

👍

[FriederikeHanssen]

I am a little confused by this one, but I don't know the tool. If I understand the input logic correctly, than the only file in the genome-folder is the kmer-fasta. Why do you need to point to it twice? From the doc it sounds like these might be different files: ```
-r, --reference=VALUE Canvas-ready reference fasta file (required)
-g, --genome-folder=VALUE folder that contains both genome.fa and
GenomeSize.xml (required)

[Schmytzi]

Canvas doesn't actually use the genome.fa file that is in the genome folder, it only reads GenomeSize.xml and uses the masked FASTA as its reference. I assume the parameters are the way they are for consistency with other Illumina tools. The module even works the same if kmer_fasta is not staged as Sequence/WholeGenomeFasta/genome.fa, so maybe it would be more straightforward to not to that?

[FriederikeHanssen]

it looks like all test scenarios end up with exactly the same output. Is this intended? Could you check that there are no mix up of files in the module?

[Schmytzi]

Canvas emits a single REF call for the region, which I would expect here regardless of optional input files. So I think that should be fine.