Replicate current NGS16S pipeline settings for barcodecop, dada2

[dhoogest]

data/dada_params_250.json is nearly identical to the current pipeline settings for the NGS16S assay, however it might be preferable to generate an assay specific params file for adjustments. At present, it seems the only place where there may need to be an adjustment is in the chimera settings. Need to confirm argument names before saying for sure.

As for barcodecop, there doesn't seem to be a way to provide alternate inputs / arguments at present. The current NGS16S assay differs in the following ways from the command as listed here:

• --min-pct-assignment=50 (lower threshold for warning)
• --qual-filter --min-qual=26 (same as default, but may be useful to expose as option here)
• no --match-filter arg (may or may not be deliberate in the NGS16S context)

One other 'feature' in the NGS16S pipeline logic is ability to specify a downsampling threshold. For indexed reads, barcodecop is used for downsampling if indicated, and there's a head -n # call if no indices present. May want to spin this last one into a separate issue.

[dhoogest]

@nhoffman let us know what you think tactics-wise re: handling the barcodecop and downsampling settings.

[dhoogest]

There's an alternate dada_params file I've added in #28. Only differences are to the removeBimeraDenovo fn.