Update processes directives to use selectors.

[ODiogoSilva]

As of version 0.31.0, nextflow throws a warning when using the process.$<process_name>.<directive> = <value> notation:

WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$trimmomatic_1_3 = <value>` with a process selector

And this syntax will be replaced with process selectors. Eventually, we'll need to update this, but doing so now would break pipelines running with nextflow <0.31.0.

The idea would be to replace the current syntax:

process.$fastqc.cpus = 4
process.$fastqc.memory = 4.GB

with something like:

process {
    withName: fastqc {
        cpus = 4
        memory = 8.GB
    }
}

[cimendes]

Additionally, with the newest version of Nextflow (version 19.07.0 build 5106) the following warning is emitted:

WARN: The channel create method is deprecated -- it will be removed in a future release

I still don't know what can be used as an alternative. Additionally, the nextflow version requirement needs to be updated because these changes will break compatibility with previous versions.

[cimendes]

So i did a little digging and what is causing this last warning are the Channel.create() methods. Stuff like ch = Channel.create() should therefore be removed. I still haven't checked if they are solely used in some templates or if they are in the engine, but it's a start.

[wanyuac]

This issue persists in version 1.4.1, and I haven't figured out any way to manually get around it.