Prepare two full datasets LFQ and TMT for the AWS tests

bigbio / quantms

Quantitative mass spectrometry workflow.

MIT License

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Prepare two full datasets LFQ and TMT for the AWS tests #177

Open ypriverol opened 2 years ago

ypriverol commented 2 years ago

Description of feature

@jpfeuffer and @ypriverol discussed that it would be great to have 2 full datasets, LFQ and TMT for the AWS tests. We need to find from the benchmark datasets we have used the best two examples. Recommendations are welcome @daichengxin

daichengxin commented 2 years ago

Done https://github.com/nf-core/test-datasets/pull/537

jpfeuffer commented 2 years ago

We need to add it to the pipeline as configs. We can use test_full_lfq, and test_full_tmt. We then should additionally include test_full_lfq as test_full for nfcore compatibility.

daichengxin commented 2 years ago

ok. DIA should need one too. PXD004684 @jpfeuffer @ypriverol ?

jpfeuffer commented 2 years ago

How long does it run?

ypriverol commented 2 years ago

Yes that one is fine. However, you must do the following:

[x] Base on my last multiomics file @daichengxin, remove other replicates in the experiment. Meaning, leave only one biological replicate or two by condition. I already removed one that a raw file was corrupted.