Pipeline of renalysis move search engines to SearchGUI.

bigbio / nf-workflows

Repository of Nextflow+BioContainers workflows

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Pipeline of renalysis move search engines to SearchGUI. #7

Closed ypriverol closed 5 years ago

ypriverol commented 5 years ago

The current way of injecting the parameters to the reanalysis pipeline is by hard-coding and re-write manually the parameters file for each search engine.It would be great if we use a general parameters file for SearchGUI.

[x] Replace msgfplus and XTandem by SearchGUI providing a global param file.
[x] Evaluate if is possible to replace xTandem with another search engine like comet or tide.

ypriverol commented 5 years ago

We probalby need to search which version of XTandem + MSGF+ SearchgUI is using.

ypriverol commented 5 years ago

@jgriss I will try to move the current pipeline from comet -> tide because comet is not yet supported in PIA.

jgriss commented 5 years ago

@ypriverol Perfectly fine with me! If you prefer, I'm happy to do this as well.

jgriss commented 5 years ago

Due to the bugs in PeptideShaker this has been abandoned