Add script recommendations

[pinin4fjords]

Propose some lines about module scripts.

@netlify /docs/guidelines/components/modules

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[pinin4fjords]

@nf-core-bot fix linting

[jfy133]

Ugh, escaping in suggestions is hard... hope you undersatnd it...

I also decided to be more strict, and require a stadnardised tempalte file naming structure (Which would require an update to deseq2/differential, let me know what you think...

[jfy133]

A few further tweaks

[jfy133]

Suggested change

	#### Script template stub
	#### Module template stub

[pinin4fjords]

@nf-core-bot fix linting

[SPPearce]

Can we reference the reason why not to use module binaries?
Personally I don't really like the interface to template, and I hate to see R scripts written with base R and the horribly clunky code to allow arguments in that way. I would suggest that we encourage the use of a seqera container with an appropriate interface package (e.g. argparse).
We could do with more explanation as to how to actualy use template, because I don't think we have that here (and the Seqera docs are almost non-existent on the topic).

I much prefer the use of in-line scripts where possible, what is the justification behind saying it can only be 20 lines?

[SPPearce]

Oh, and some examples pointing to other modules rather than deseq2/differential repeatedly would be good.

[christopher-hakkaart]

Can we reference the reason why not to use module binaries? Personally I don't really like the interface to template, and I hate to see R scripts written with base R and the horribly clunky code to allow arguments in that way. I would suggest that we encourage the use of a seqera container with an appropriate interface package (e.g. argparse). We could do with more explanation as to how to actualy use template, because I don't think we have that here (and the Seqera docs are almost non-existent on the topic).

A PR is in progress to address the gap in the Nextflow docs. This doesn't mean that nf-core can't have its own standards/recommendations, but it will hopefully add something that can be easily referenced.

[SPPearce]

Can we reference the reason why not to use module binaries? Personally I don't really like the interface to template, and I hate to see R scripts written with base R and the horribly clunky code to allow arguments in that way. I would suggest that we encourage the use of a seqera container with an appropriate interface package (e.g. argparse). We could do with more explanation as to how to actualy use template, because I don't think we have that here (and the Seqera docs are almost non-existent on the topic).

A PR is in progress to address the gap in the Nextflow docs. This doesn't mean that nf-core can't have its own standards/recommendations, but it will hopefully add something that can be easily referenced.

Great, always happy to see more documentation on the Nextflow page itself.

[jfy133]

Can we reference the reason why not to use module binaries?

Apparently you can only use binaries in cloud contexts if you use wave (not other containers), which I feel is overly restrictive.

Personally I don't really like the interface to template, and I hate to see R scripts written with base R and the horribly clunky code to allow arguments in that way. I would suggest that we encourage the use of a seqera container with an appropriate interface package (e.g. argparse). We could do with more explanation as to how to actualy use template, because I don't think we have that here (and the Seqera docs are almost non-existent on the topic).

Agree, more Nextflow docs/example on how to use would be nice, and again, would rather not 'force' Seqera Containers.

I much prefer the use of in-line scripts where possible, what is the justification behind saying it can only be 20 lines?

It's a rule of thumb suggested by @pinin4fjords (I've changed to 'approx' though)

Oh, and some examples pointing to other modules rather than deseq2/differential repeatedly would be good.

Suggest some then! 😝

[christopher-hakkaart]

I suggest removing the repeated "approximately 20 lines" and instead describing this once: something like, "When a script extends beyond a readable length (approximately 20 lines)..."

Then just refer to a readable length for the rest of the text.

Readable length could be "Manageable size", "too verbose", "excessive length", or something like that

[jfy133]

I suggest removing the repeated "approximately 20 lines" and instead describing this once: something like, "When a script extends beyond a readable length (approximately 20 lines)..."

Then just refer to a readable length for the rest of the text.

Readable length could be "Manageable size", "too verbose", "excessive length", or something like that

Done!

[christopher-hakkaart]

Much better - thanks!

[pinin4fjords]

@SPPearce to be clear, I want module binaries to be the way to do this, with argparse baked into the container to avoid all that junk I have to put in templates, I'm no template fanboy.

But module binaries are not entirely portable (see the provisos in the linked docs), so templates are the least worst way of doing this I've found - overjoyed if someone tells me a better way.

My crappy outdated R is another issue entirely ;-)

[christopher-hakkaart]

Is everyone reasonably happy with the current PR? Are there any blockers to merging?