refactor: Update output locations and include fibertools "all" output

fiberseq / fiberseq-smk

Snakemake pipeline for processing fiberseq data

https://fiberseq.github.io/fiberseq-smk/

MIT License

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Closed mrvollger closed 1 year ago

mrvollger commented 1 year ago

This pr updates output locations of files to include the sample name and simplify and now also includes fibertools "all" output.

If you rerun and old run of the pipeline with the new code an error message asking you to move the important files:

Example output dir with sample name test:

And I have made sure it runs the test case from end to end.

@sjneph could you look over the changes and let me know if there is anything you disagree with?

mrvollger commented 1 year ago

@sjneph I made more changes, that are basically just reorganizing code.