mhcquant
mhcquant copied to clipboard
nf-core
Identify and quantify MHC eluted peptides from mass spectrometry raw data
### Description of feature I'm running the `dev` branch of `mhcquant` under the test profile on my local server: ```bash git clone --branch dev --single-branch [email protected]:nf-core/mhcquant.git mhcquant nextflow run ./main.nf...
### Description of the bug I have problems using MHCquant with multiple variable modifications. The whole pipeline works when not specifying any modifciations. With multiple modifcations, the pipeline only works...
### Description of the bug Hi, I got an error in the first step, 'profile test'. Here is the relevant report. Maybe there is something wrong with my singularity. ###...
### Description of the bug When there are no significant hits after FDR filtering, the metadata of the file so no longer printed. The output prints "null" for the sample...
### Description of feature We need to test `TDF2MZML` and all the downstream processes. We can now use [this recently published data](https://www.ebi.ac.uk/pride/archive/projects/PXD038782) to test bruker files.
### Description of feature We should make sure to share as much modules as possible with other nf-core repositories using these tools. E.g. https://github.com/nf-core/quantms/issues/63 This issue tracks the progress of...
### Description of feature As there is hardly any useful information in the QC, I would like to include a better functionality. Additionally, it would be of interest would be...
### Description of feature Make sure that the outcome TSV is changed to a more readable format since this content is not ready to be used for analysis immediately. A...
### Description of feature Since the reader and writer in MS2Rescore are based on psm_utils and psm_utils [is now capable](https://github.com/compomics/psm_utils/pull/52) of reading and writing idXML files, we should replace it...
### Description of feature Currently compression types tar / zip are not supported. There are nf-core modules that can simply be plugged in.