Simplify samshee module

[grst]

Description of feature

Sameshee now has a proper CLI implemented, see
https://github.com/lit-regensburg/samshee?tab=readme-ov-file#commandline-tool

With that, I think we should

• get rid of the custom python script
• turn samshee into a nf-core/modules module.

[grst]

I think this is a bit higher priority now as I had a samplesheet that failed (and shouldn't) with samshee v0.1.12, but passes with v0.2.0.

In particular, lines like

[Header]
Description,,,,,,,,

that have an empty value in col2 led to an error.

So let's prioritize this and make a samshee v0.2.0 module please.

@apeltzer @atrigila @nschcolnicov

[nschcolnicov]

Created a PR for this: @grst @atrigila nf-core/modules#6749. Let me know what you think.

[grst]

It wasn't evident for me what's the default logic of the samshee CLI so I did some digging:

• When the output format of samshee is Illumina v2, it will always validate the samplesheet as Illumina V2 sheet, even when no --schema option is present.
• Therefore, a V1 samplesheet will always fail unless --output-format sectioned is given. People with V1 samplesheets can either skip samshee altogether or specify this as a tool option. Either way, samshee doesn't properly validate V1 samplesheets except that the content is parseable since there is no suitable schema available until now). I think this is OK behavior as long as this is properly documented.
• The samplesheet could have not data section and still be valid. If we want to catch that, we'd need to add --schema '{"required": ["BCLConvert_Data"]}'. We can discuss if we should enable certain rules in the pipeline by default, but the standard V2 samplesheet logic is probably already a good start.

[nschcolnicov]

Sorry for taking so long to get back to you, I was focused on the template update. Regarding the output-format sectioned , I tested it on the test profile for example and it still makes it fail. Regardless this is something we could add to the pipeline by having a parameter such as "samplesheet_version" that can set this argument on and off depending on its value.