proteomicslfq

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Once an API is available. @ypriverol

jpfeuffer

[FEATURE] xtandem support (beta)

1

First try to include XTandem as another search engine.

jpfeuffer

E.g. different enzymes. Note that e.g. Comet can directly search with a second enzyme. The difficulty is that you usually need to specify if the enzyme was applied after each...

jpfeuffer

Comet search with Lys-C digestion fails

5

My pipeline fails when using Lys-C as a digestion enzyme, ```NT=Lys-C;AC=MS:1001309 ``` or ```NT=Lys-C/P;AC=MS_1001310```. It works with trypsin ```NT=Trypsin;AC=MS_1001251```. My command is: ``` nextflow run nf-core/proteomicslfq -r 43c77e5 -profile singularity...

ncarrut

Some errors while processing a QC HeLa file

1

Hi, Congratulations for the 1.0.0 release! I'm testing it with a QC HeLa sample but I got some errors. Could you help me? Thanks! ``` nextflow N E X T...

rolivella

Allow "per-sample" processing

2

Useful for huge studies where the samples are actually unrelated. Unrelatedness could be one or more of the following: - Different number of fractions - Different instruments - Unrelated conditions...

jpfeuffer

This would introduce a for-loop around ProteomicsLFQ with the contrasts you actually want to test. That: a) you reduce memory consumption significantly since not all maps are loaded and aligned...

jpfeuffer

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

1

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...

jpfeuffer

Restart with peakpicking openms

3

@jpfeuffer sometimes the pipeline fails in the id part because of the peak-peaking step by the ThermoRawFileParser. Would be great to "restart" the pipeline, same parameters but with the openms...

ypriverol

- Address remaining TODOs. - Adhere to nextflow coding standard by prefixing all channels with ch (required by some code highlighters).

jpfeuffer