nf-core/mhcquant

Issues

• mhcquant fails possibly due to ms2pip

  #336 opened 25 days ago by shubham1637
  16

• Create spectrum library from DDA runs

  #330 opened 2 months ago by jonasscheid
  1

• Global-FDR support

  #331 opened 2 months ago by jonasscheid
  0

• Alter tsv outcome

  #291 opened a year ago by marissaDubbelaar
  1

• Add MS1 Chromatogram to multiQC

  #328 opened 2 months ago by jonasscheid
  0

• Port local OpenMS modules to nf-core modules

  #296 opened a year ago by jonasscheid
  0

• Add OpenMS IDMassAccuracy module

  #327 opened 2 months ago by jonasscheid
  1

• "No significant hits found" message (dev branch)

  #305 opened 5 months ago by steffenlem
  1

• Support compressed input

  #281 opened 5 months ago by jonasscheid
  1

• Add tests for bruker files

  #306 opened 5 months ago by jonasscheid
  1

• Create only one decoy database if no vcf_sheet is given

  #287 opened 5 months ago by jonasscheid
  0

• Class1 prediction folder is empty

  #278 opened 5 months ago by jonasscheid
  0

• Update Fred2 to epytope

  #245 opened 5 months ago by marissaDubbelaar
  0

• Adding generated proteins to reference database is erroneous

  #248 opened 5 months ago by jonasscheid
  3

• Use IDfilter when OpenMS 3.1.0 is released instead of pyopenms IDfilter

  #283 opened 5 months ago by jonasscheid
  0

• Replace DeepLC and MS2PIP wrappers with MS2Rescore

  #288 opened 5 months ago by jonasscheid
  0

• DEEPLC and MS2PIP doesnt work with multiple variable modifications

  #294 opened 5 months ago by yannic-chen
  6

• Add cache management for `ms2rescore`

  #317 opened 5 months ago by MajoroMask
  0

• error from '-profile test'

  #309 opened 6 months ago by sundysun99
  3

• URGENT: pin nf-validation version

  #308 opened 7 months ago by nvnieuwk
  4

• Better multiQC report

  #290 opened a year ago by marissaDubbelaar
  0

• Re-itterate over the contributors

  #289 opened a year ago by marissaDubbelaar
  0

• Remove writing out all peaks when using Ion Annotator

  #286 opened a year ago by jonasscheid
  0

• Include OpenMS FileInfo to check for valid mzML files

  #240 opened a year ago by jonasscheid
  3

• Handling the case when no significant hit where found

  #246 opened a year ago by steffenlem
  0

• Duplicate peptide identifications

  #250 opened a year ago by steffenlem
  6

• Add support for bruker files

  #263 opened a year ago by jonasscheid
  0

• Update to new openMS version 3.0.0

  #265 opened a year ago by jonasscheid
  0

• Add support for sdrf input

  #277 opened a year ago by jonasscheid
  0

• MapRTTransformer does not change RT according to trafoXML

  #276 opened a year ago by jonasscheid
  6

• Process labeled data

  #231 opened a year ago by jonasscheid
  1

• Inconsistent annotation fdr_level parameters

  #228 opened 2 years ago by marissaDubbelaar
  0

• Profile test and test_full cannot access ref database

  #233 opened 2 years ago by jonasscheid
  4

• DecoyDatabase uses tryptic configuration to generate decoys

  #255 opened 2 years ago by jonasscheid
  0

• Add low-resolution test data

  #261 opened 2 years ago by jonasscheid
  0

• FATAL: container creation failed: mount error: while mounting: destination doesn't exist in container

  #251 opened 2 years ago by charmoniumQ
  4

• Issue ion annotator feature

  #236 opened 2 years ago by marissaDubbelaar
  0

• Make ion annotation optional

  #235 opened 2 years ago by jonasscheid
  0

• Issue in the MzTabExporter

  #230 opened 2 years ago by marissaDubbelaar
  4

• Ion identification within a mass spectrum

  #220 opened 2 years ago by polklin
  2

• Issue annotation of the HLA alleles in parameters

  #241 opened 2 years ago by marissaDubbelaar
  0

• Comet: theoretical_fragment_ion parameter missing

  #225 opened 2 years ago by jonasscheid
  1

• Changes to the params documentation

  #193 opened 3 years ago by WackerO
  0

• Missing mzTab files

  #211 opened 3 years ago by marissaDubbelaar
  0

• problem --fixed_modification

  #212 opened 3 years ago by marissaDubbelaar
  0

• Retrieve ID for output of unquantified data

  #190 opened 3 years ago by marissaDubbelaar
  0

• Output documentation

  #199 opened 3 years ago by WackerO
  0

• Samplesheet format `Usage.md`

  #192 opened 3 years ago by SusiJo
  0

• Remove TOC `Usage.md`

  #191 opened 3 years ago by SusiJo
  0

• Add backslashes to run command

  #189 opened 3 years ago by SusiJo
  0