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nf-core / proteomicslfq

Proteomics label-free quantification (LFQ) analysis pipeline
https://nf-co.re/proteomicslfq
MIT License
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Refine defaults and fallbacks in engine parameters #54

Open jpfeuffer opened 4 years ago

jpfeuffer commented 4 years ago

e.g. in SDRF we usually have the tolerances, their units, and the instrument name.

BUT: The search engines have restrictions. They usually take only high_res vs low_res for some additional settings. Comet only allows for Da as unit in the fragment_bin_tolerance.

See #53 for a first step.

ypriverol commented 4 years ago

@jpfeuffer I have seen in most of the high-res instrument 0.05 Da rather than 0.01

jpfeuffer commented 4 years ago

I think the defaults are relatively sane right now but we probably should revisit after some more testing. For example, I am not sure about activation_method/fragment_method. MSGF and Comet support different things here.