Warn and fail if an experimental design is specified together with an SDRF as --input

nf-core / proteomicslfq

Proteomics label-free quantification (LFQ) analysis pipeline

https://nf-co.re/proteomicslfq

MIT License

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Warn and fail if an experimental design is specified together with an SDRF as --input #112

Open jpfeuffer opened 3 years ago

jpfeuffer commented 3 years ago

We could also overwrite the experimental design generated from the SDRF but I don't know if that gets even more confusing. Maybe in the long run we even deprecated the "--expdesign" parameter and require an SDRF? But the "--input foo.mzML --expdesign des.tsv" is just very convenient for quick analyses.

ypriverol commented 3 years ago

I think we should promote the SDRF, go in favor of a standard file format that would enable more reanalysis and public data annotation. Deprecate the --expdesign. 💪