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dereneaton / ipyrad

Interactive assembly and analysis of RAD-seq data sets
http://ipyrad.readthedocs.io
GNU General Public License v3.0
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Step 2: Any samples failing kill this entire step #390

Closed isaacovercast closed 4 years ago

isaacovercast commented 4 years ago

Step2.run() calls remote_run_cutadapt which runs cutadapt on all samples after which it pulls the results for each sample. If any sample fails then the entire step fails, which is antagonizing. If samples fail these should be recorded and reported to the user, and the samples that don't fail should be allowed to finish.

I'm not sure how straightforward this would be because Step2.assembly_cleanup() calls self.data._build_stat("s2"), which will also fail and raise for samples that don't have 's2' stats. :-/

isaacovercast commented 4 years ago

nvm, the call to _build_stat("s2") won't raise, it'll be fine.

isaacovercast commented 4 years ago

I fixed this so it catches any samples that fail this step and writes out sample names and error messages to a log file in the _edits directory.