Fix ref genomes & other behaviour

[apeltzer]

Trying to fix couple of stuff , e.g. fasta reference naming, indexing availability without channels so we can re-use them efficiently.

PR checklist

• This comment contains a description of changes (with reason)
• If you've fixed a bug or added code that should be tested, add tests!
• If necessary, also make a PR on the nf-core/eager branch on the nf-core/test-datasets repo
• Ensure the test suite passes (nextflow run . -profile test,docker).
• Make sure your code lints (nf-core lint .).
• Documentation in docs is updated
• CHANGELOG.md is updated
• README.md is updated

Learn more about contributing: https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md

[maxibor]

Looks good to me for merging if Travis says bueno

[apeltzer]

Yeah, just the indexes missing 👍 I'll also try to go back supporting whatever kind of index is provided by users.... Fa, Fasta, fn, all good for me :....

[apeltzer]

This now uses value channels for input fasta files, that are not consumed. Additionally, I cleaned up the code quite a bunch 👍

[jfy133]

The previous approve was a mistake - but mobile github site doesn't give me an option to revoke... I'll test your personal branch tonight

[apeltzer]

One missing thing is gz input for fasta but I am almost there - maybe after dinner or tomorrow. Everything else should work

[phue]

Wasn't there some problem with using the file method because input files lying on different filesystems were not staged properly? I remember something along these lines which made us switch to channels for everything.

[apeltzer]

It was, but I talked to Paolo and apparently that is not true and was probably a misconfiguration on our side with Singularity missing required bind paths - so one can assume this approach works fine.