Remove Input Upload repeat in Denoise step

[kshen3778]

Currently, the Denoise step repeats the Input Upload step again (the inputs are both a manifest file). Instead, the Denoise step should be taking the qza that's the output of the input upload step as its input.

[kshen3778]

We found out that the manifest file from the Input Upload step is required for the Denoise step. You can't just only input a qza into Denoise.

"Because a manifest can contain multiple runs, it’s possible for there to be multiple qza files created as the result of the Input Upload step. Because of this, I’m going to keep the input for the Denoise step a manifest file instead of a single .qza since AXIOME need the runIDs in the manifest file to keep track of the files in case of multiple runs (the path Denoise will search for will be something like outputdir/{runID}_paired_end_demux.qza).

From looking at the code, the multiple run import would produce multiple qza files (one per run), not a single one: run1_paired_end_demux.qza, run2_paired_end_demux.qza, etc. If the manifest only contains one run, the the qza would just be paired_end_demux.qza without mention of the runID.

The reason runIDs is needed in Denoise, is because the names of the qza files contains the runIDs, and the only piece of data that contains the runIDs is the manifest. Of course, I think in the future once we could create a AXIOME config file that could hold the runIDs, but I think that would be later when we get to implementing the new session management."

Denoise step also does merging of demux files.