Repalce channel.fromFilePairs() with samplesheet #32
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Signed-off-by: Ben Sherman <[email protected]>
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Closing in favor of #34 . Technically not a preview feature, so these changes should be safe to merge into |
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This PR replaces the use of
channel.fromFilePairs()with a samplesheet.The
fromFilePairsfactory 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.