Nextflow installation improvements

Five years ago there was a closed bug that was asking for Nextflow to be incorporated into Homebrew. After watching my team of mixed skillsets, scientists and engineers, struggle though a series of installation issues, I think it might be worthwhile to revisit this.

Nextflow has dependencies, and some of them are unusual like specific implementations of OpenJDK. A package manager will manage these dependencies, giving them executable access, and linking them.

The current installation strategy is to use wget (not installed by default on MacOS) to download a bash script with suppressed output, which runs a Nextflow installer script with debug messaging turned off. When this runs, the console hangs, and because of underlying bugs with other dependencies (Capsule), it can never return — or print anything. I think this is not the right installation strategy for Nextflow anymore. Folks that tried using SDKMAN! (also installed with arbitrary downloaded code execution) ran into linking issues where their PATH didn't have Java linked up or JAVA_HOME set.

I think brew install nextflow yum install nextflow and apt-get install nextflow would all be very useful depending on the platforms folks are working on. If that's too much, the folks on non-mac unix variants probably have the required skillset to work around the issues they are likely to run into, but scientists working on MacBooks are less likely to be able to navigate this. So if just Homebrew was supported, I think that would make a huge difference.

Thank you,
Ben

Start by reviewing the current wget-downloaded Bash installer and its Java, OpenJDK, Capsule, and PATH/JAVA_HOME dependencies. Compare the installation problems described here with the scope of supporting Homebrew, yum, or apt-get, and define done as a reliable, observable installation path for the selected platforms.