nf-core/epitopeprediction

Issues

• epitopeprediction using mhcflurry vs running directly mhcflurry

  #263 opened 2 months ago by gianfilippo
  2

• Add bcftools stats with multiQC

  #267 opened 2 months ago by jonasscheid
  0

• isSynonymous issue

  #265 opened 2 months ago by zhenzuo2
  0

• KeyError: 'Coding sequence'

  #255 opened 2 months ago by gianfilippo
  7

• Peptides are sometimes removed in the output when an unmodified sequence in present in the input

  #258 opened 2 months ago by steffenlem
  0

• BioMart request declined

  #248 opened 4 months ago by zhenzuo2
  5

• Ensemble archive GRCh38 is out of date (apr2018)

  #208 opened a year ago by tlitfin
  7

• show_supported_models module not called correctly

  #224 opened a year ago by jonasscheid
  1

• variant details not shown in epitope prediction result tsv when using VEP as annotation tool

  #240 opened a year ago by qbicStefanC
  2

• Check sample sheet doesn't use RowChecker class

  #206 opened a year ago by jonasscheid
  0

• Add Manta support for structural variant prediction

  #181 opened 2 years ago by jonasscheid
  2

• Update general structure of MHCbinding subworkflow

  #205 opened 2 years ago by alina-bauer
  0

• Add syfpeithi module

  #217 opened a year ago by jonasscheid
  0

• Add netmhc(ii)pan module

  #216 opened a year ago by jonasscheid
  0

• Add mhcflurry module

  #215 opened a year ago by jonasscheid
  0

• Add mhcnuggets module

  #214 opened a year ago by jonasscheid
  0

• Rewrite and move check_requested_models in input_check subworkflow

  #207 opened 2 years ago by jonasscheid
  0

• Version 2.2.0 does not produce any predictions anymore for netmhcpan class 1

  #195 opened 2 years ago by steffenlem
  3

• Proteome CLI flags of epaa and nextflow differ

  #201 opened 2 years ago by jonasscheid
  2

• Use nf-core modules

  #193 opened 2 years ago by ggabernet
  0

• Issue with the process: EXTERNAL_TOOLS_IMPORT

  #183 opened 2 years ago by marissaDubbelaar
  3

• Add support for VEP annotated files

  #172 opened 2 years ago by christopher-mohr
  0

• proper inplementation of the current netmhc_tools_import process

  #99 opened 3 years ago by marissaDubbelaar
  4

• Use Epytope instead of Fred2 once the release is available

  #130 opened 3 years ago by ggabernet
  0

• Neoepitopeprediction is too memory demanding

  #140 opened 3 years ago by jonasscheid
  1

• KeyError: 'Transcript ID'

  #146 opened 3 years ago by marissaDubbelaar
  2

• Extend binding threshold with rank metric

  #160 opened 3 years ago by jonasscheid
  0

• Add RNAseq table as input

  #134 opened 3 years ago by ggabernet
  1

• nfcore module: csvtk_concat or cat (mergeResults)

  #97 opened 3 years ago by marissaDubbelaar
  0

• Missing output information in neoepitopeprediction snvs and indels

  #141 opened 3 years ago by jonasscheid
  2

• Splitting a zipped vcf.gz file

  #143 opened 3 years ago by marissaDubbelaar
  0

• Neoepitopeprediction crashes when a variant has annotated metadata, which is not available for others

  #136 opened 3 years ago by jonasscheid
  0

• Reorganize result folder structure

  #131 opened 3 years ago by christopher-mohr
  0

• No attribute 'MIN_DP'

  #142 opened 3 years ago by marissaDubbelaar
  1

• Create mulled container that can be used for the PEPTIDE_PREDICTION

  #91 opened 3 years ago by marissaDubbelaar
  5

• Implementation of the sample sheet in the pipeline

  #102 opened 3 years ago by marissaDubbelaar
  8

• local module: csvtk_split and snpsift_split (splitVariants)

  #93 opened 3 years ago by marissaDubbelaar
  5

• Port workflow to DSL2

  #89 opened 3 years ago by christopher-mohr
  1

• local module: check_requested_models

  #92 opened 3 years ago by marissaDubbelaar
  2

• local module: genPeptides

  #94 opened 3 years ago by marissaDubbelaar
  2

• Local module: splitPeptides

  #95 opened 3 years ago by marissaDubbelaar
  2

• local module: peptidePrediction

  #96 opened 3 years ago by marissaDubbelaar
  2

• nfcore module: cat (mergeFastas)

  #98 opened 3 years ago by marissaDubbelaar
  1

• local module: mergeReports

  #101 opened 3 years ago by marissaDubbelaar
  1

• Template update for nf-core/tools v2.1

  #100 opened 3 years ago by christopher-mohr
  1

• Alter the tests so that a sample sheet can be used as input instead of one file

  #103 opened 3 years ago by marissaDubbelaar
  2

• Update the docs based on the changes

  #106 opened 3 years ago by marissaDubbelaar
  1

• new nfcore module of SNPSIFT_SPLIT

  #104 opened 3 years ago by marissaDubbelaar
  0

• new nfcore module of CSVTK_SPLIT

  #105 opened 3 years ago by marissaDubbelaar
  0

• Possibly: create a mulled version of the container (Fred2, mhcflurry, mhcnuggets)

  #90 opened 3 years ago by marissaDubbelaar
  0