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Zymo-Research / figaro

An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters
GNU General Public License v3.0
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missing nameless outputs #27

Closed handibles closed 3 years ago

handibles commented 3 years ago

Sent a PR , but there are two other non-critical snags that are probably better mentioned here (possible related to the PR):

  1. firstly, from 132 fastqs, I get back 118 entries in the JSON output (log is empty), suggesting some files are silently failing (same run, same naming convention). I would check the missing files, but see 2:
  2. no names are appended to the outputs in the JSON - not sure if this is intended functionality.

Partially due to 1&2, I'll probably end up taking subjective averages of these objective parameters output - can I ask what is the envisioned next step for e.g. a DADA2 run incorporating this data (esp. in JSON)? Pass values to filtAndTrim() as a vector of parameters?

As ever Dev, thanks for the time put into this.

handibles commented 3 years ago

drat, spotted duplicate issue in list. Will defer there, see issue #25

michael-weinstein commented 3 years ago

I think I fixed some of the more critical issues related to this. Going to see about making some bigger changes in a version 2 that should allow for some variability in the read-lengths.