Repalce channel.fromFilePairs() with samplesheet

[bentsherman]

This PR replaces the use of channel.fromFilePairs() with a samplesheet.

The fromFilePairs factory should not be encouraged because it requires knowing how files are organized in a directory tree, and it isn't flexible enough to support arbitrary metadata.

This work aligns with #31 to model more clearly the inputs and outputs of a pipeline. Notably, the input is a samplesheet and the output is another samplesheet. These two PRs lay the groundwork for static types and pipeline chaining.

I have tried to keep the code as simple as possible while demonstrating best practices for workflow inputs.

[bentsherman]

@jorgee this PR should make it easier to generate a samplesheet with many (small) samples. Combine it with #30 or #31 and you should have a good stress test for the CID store.

[bentsherman]

Closing in favor of #34 . Technically not a preview feature, so these changes should be safe to merge into master at any time