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TalusBio / nf-encyclopedia

A NextFlow pipeline for chromatogram library DIA proteomics workflows
Apache License 2.0
6 stars 4 forks source link

Add `-frag HCD` to EncyclopeDIA local searches #9

Closed wfondrie closed 2 years ago

wfondrie commented 2 years ago

This is not the main issue we're running into, but will improve our results a bit.

ricomnl commented 2 years ago

I think the 'local_options' would be overwritten by our pipeline launcher, no? Should we add this feature in the pipeline launcger repo instead?

wfondrie commented 2 years ago

Do we specify local_options with the pipeline launcher? In that case, we should update it there too!

ricomnl commented 2 years ago

Just checked, we're actually not doing this yet. Up to you, we can either merge this PR and leave it for now, or add the feature to teh pipeline launcher. I'm fine with either