Remove for loops from the pipeline template

[bentsherman]

for and while loops will not be supported in the strict parser that is on the way. Looks like #3166 addresses one of them, here are a few more.

In workflowCitation():

    // old
    for (String doi_ref: manifest_doi)
        temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"

    // new
    manifest_doi.each { doi_ref ->
        temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
    }

I believe the other for loops in utils_nfcore_pipeline can be addressed in a similar way.

The one in checkCondaChannels() is a bit trickier because it's not just iterating through a list:

    def n = required_channels_in_order.size()
    for (int i = 0; i < n - 1; i++) {
        channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1]))
    }

I believe the intent is to make sure that the required channels are in the right order while also allowing other channels to be in the list. Here is a "groovier" 😉 way to do it:

    def channel_priority_violation = required_channels_in_order != channels.findAll { ch -> ch in required_channels_in_order }

[mirpedrol]

Hi, this was fixed by @nvnieuwk, the current code looks like this:

manifest_doi.each { doi_ref ->
        temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
    }

and

required_channels_in_order.eachWithIndex { channel, index ->
        if (index < required_channels_in_order.size() - 1) {
            channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index+1]))
        }
    }

Does this look ok?

[bentsherman]

Looks fine to me! Just don't forget the other for loops in utils_nfcore_pipeline, there were several more that I didn't list

[mirpedrol]

Done with #3166, thanks!