Add primerprospector_analyzeprimers

[vagkaratzas]

Workaround shim in main:

Primer Prospector 1.0.1 (this is an old codebase) is a Python 2 package and the BioContainer entrypoint uses Python 2.7.
The bug is specifically Python 2 behavior: range() requires integer arguments, and the package passes a
numpy.float64 during plotting.

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[timrozday-mgnify]

Thanks @vagkaratzas ! This looks useful.

I have one major issue with this module relating to incorrect handling of output hit files when there are multiple primers in the input primer file (a common case). The tests should be amended with this case.

I think it would be useful to support gzipped fasta inputs, but I don't know what nf-core good practice says about that.

[timrozday-mgnify]

For multiple primers in the input primer file this will cause an error or overwrite some results. Rather all the files should be emitted in the hits output channel. If prefix renaming is desired then it needs to be performed on each of the produced hits files.

[vagkaratzas]

Good catch, updated!

[vagkaratzas]

I think it would be useful to support gzipped fasta inputs, but I don't know what nf-core good practice says about that.

Since the module allows a list of fasta files (and not just a single fasta one), it is a bit more complicated to do that in the code (but definitely not impossilbe). But for now I guess running GUNZIP as an intermediate step can solve that case. The module is already a bit more complicated than usually (due to being old and possibly unreachable authors to update), so I'd leave the decompressing out of the current scope.

[timrozday-mgnify]

Looks great, thank you @vagkaratzas!

Just two edits to the error messages since prefix is no longer used to rename output files.

I've approved so you can crack on with merging when you choose.