mhcquant
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nf-core
Identify and quantify MHC eluted peptides from mass spectrometry raw data
### Description of feature Currently, ion annotations of sample-condition runs are written in two files: `*_all_peaks.tsv` and `*_matching_ions.tsv` Since peak information can be read out from an indexed mzML file,...
### Description of feature Currently the pipeline computes for each unique sample-condition a decoy database. But this behaviour is only needed if vcf_sheet is specified. Fixing this would reduce the...
### Description of feature Waiting for release, since [this](https://github.com/OpenMS/OpenMS/pull/7021) has recently been included. We need keepBestPerPeptide filter to handle merged files in quant workflow
### Description of feature The Sample-Data relationship file format (sdrf) has been introduced at [HUPO-PSI](https://psidev.info/magetab). With this addition we could reprocess PRIDE projects that have been annotated with this novel...
### Description of the bug If I run `test_full` with `predict_class_1` I don't get any binding scores in the outputs. We wait until epitopeprediction subworkflow is finished to use it...
### Description of feature With the new functionalities that Epytope has to offer, it would be of interest to update the afflicted scripts to Epytope
### Description of the bug The process `GENERATE_PROTEINS_FROM_VCF` and the underlying script `variants2fasta.py` need to get a complete overhaul. A few issues I ran into: - At least [variant of...