Small improvements to add additional context/explanations

[ejseqera]

Optional enhancement: Added additional context to the body and notes to provide clearer explanations around concepts such as tuples and the handling of accessory files.

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[mribeirodantas]

I agree it's an improvement, but the ending worries me a bit. They will be converted into channels implicitly so I think there should be a better way to express the last mention of channels in the new version. What do you think?

[pinin4fjords]

Yeah, I'm with @mribeirodantas on this one. I actually don't like the bare file() syntax, because of the implicit channel creation I don't think there's a principled reason to use it (besides maybe if you want to include the same file in multiple channels while initialising it once). So I disagree even with the original text - it's just a laziness/ convenience thing.

I'd rather we encouraged explicit channel creation, because I think it's easier to read.

[ejseqera]

I see your points. I believe that there’s room to provide more context for newer developers about when and why to use the file() syntax in scenarios like this. How about reframing it like this:

"While main data inputs are streamed dynamically through channels, there are two approaches for handling accessory files. The recommended approach is to create explicit channels, which makes data flow clearer and more consistent. Alternatively, the file() function to create variables can be used for simpler cases, particularly when you need to reference the same file in multiple processes - though be aware this still creates channels implicitly. For example: ..."

This way, we emphasize explicit channel creation as the best practice while still introducing file() as an alternative for convenience. Do you think this balances the guidance appropriately?

[mribeirodantas]

That's an improvement! I keep wanting to throw in the queue/value channel concepts but for very beginners, I think they get more in the way than help 😆. What about a shorter but direct version, like:

Main data inputs are streamed through channels, but accessory files that will be used together with multiple different samples can be handled in two ways:

* Recommended: Use explicit channel factories such as `Channel.value` for clear and consistent data flow.
* Alternative: Use the file() function. Note that this creates a channel implicitly.

[adamrtalbot]

What happened was:

1. We initially just used params.fasta as inputs, which are magically turned into value channels...sometimes. This worked but users found it confusing when it didn't work on their pipelines.
2. Followed by Channel.of(params.fasta).collect() which opened up a whole conversation about queue vs value channels which was just unecessary.
3. Using file is the most convenient way of doing it, but always prompts the question why file vs channel.

In the future, value channels will be deprecated and file will be the main way of doing this, so I think it makes sense to use file for now with with @ejseqera explanation included.

[pinin4fjords]

In the future, value channels will be deprecated and file

TIL. What about single-value non-file channels?

[adamrtalbot]

In the future, value channels will be deprecated and file

TIL. What about single-value non-file channels?

What about them?

names = Channel.of('adam', 'jon', 'marcel')
greeting = "hello"

GREETING(greeting, names)