the current tide workflow mzidentml is not valid

bigbio / nf-workflows

Repository of Nextflow+BioContainers workflows

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the current tide workflow mzidentml is not valid #12

Open ypriverol opened 5 years ago

ypriverol commented 5 years ago

We need to solve the issue with the mzIdentML production that is not valid.

[ ] First option: I will contact the developers to see if they are willing to make them happen.
[ ] Second Option: Export to PepXML and develop a reader of PepXML in PIA.
[x] Third Option: Use the txt file in the pipeline and extend PIA.

ypriverol commented 5 years ago

The export using txt works but PIA has some wrong behaviour . Im fixing now the bugs.

ypriverol commented 5 years ago

I have removed for now the mzidentml export and use the txt file output that works perfectly well. I have created an issue in tide repo to address the mzidentml issues. check here: https://github.com/crux-toolkit/crux-toolkit/issues/423 . We should close this issue only when everything with the mzidentml is fine.