Error When converting to OpenMS enzymes

[ypriverol]

When Lys-C/P to OpenMS enzyme, We transform to sentence style (Lys-c/p), However, OpenMS uses Sentence and Camel combined. This definition

sdrf-pipelines/sdrf_pipelines/openms/openms.py

Line 126 in 07c1dea

self.enzymes = {

must be extended.

export SAGE_LOG=trace
  SageAdapter \
      -in 170830_04_Orbi2_SK_IN_G240_T275_TYTI_Int_Std_UPS2_BSA_top10.mzML 170830_04_Orbi2_SK_IN_G240_T275_TYTI_Int_Std_UPS2_BSA_top5.mzML 170911_04_Orbi2_SK_IN_G240_T275_TYTI_Int_Std_UPS2_BSA_top10.mzML 170911_04_Orbi2_SK_IN_G240_T275_TYTI_Int_Std_UPS2_BSA_top5.mzML 170929_04_Orbi2_SK_IN_G240_T275_TYTI_Int_Std_UPS2_BSA_top10.mzML 170929_04_Orbi2_SK_IN_G240_T275_TYTI_Int_Std_UPS2_BSA_top5.mzML \
      -out out_0_sage.idXML \
      -threads 15 \
      -database "uniprotkb_Saccharomyces_cerevisiae_AND_51_UPS_2024_04_05_decoy.fasta" \
      -decoy_prefix DECOY_ \
      -min_len 6 \
      -max_len 40 \
      -min_matched_peaks 1 \
      -min_peaks 1 \
      -max_peaks 500 \
      -missed_cleavages 2 \
      -report_psms 1 \
      -enzyme "Lys-c/p" \
      -precursor_tol_left -20.0 \
      -precursor_tol_right 20.0 \
      -precursor_tol_unit ppm \
      -fragment_tol_left -20.0 \
      -fragment_tol_right 20.0 \
      -fragment_tol_unit ppm \
      -fixed_modifications 'Carbamidomethyl (C)' \
      -variable_modifications 'Acetyl (Protein N-term)' 'Deamidated (N)' 'Deamidated (Q)' 'Oxidation (M)' \
      -max_variable_mods 3 \
      -isotope_error_range 0,1 \
      -PeptideIndexing:IL_equivalent \
      -PeptideIndexing:unmatched_action warn \
      -debug 0 \
       \
      2>&1 | tee out_0_sage.log
  
  if [[ 6 -ge 2 ]]; then
      IDRipper -in out_0_sage.idXML -out . -split_ident_runs
      rm out_0_sage.idXML
      for f in *.idXML
      do
          mv "$f" "${f%.*}_sage.idXML"
      done
  fi
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_QUANTMS:QUANTMS:LFQ:ID:DATABASESEARCHENGINES:SEARCHENGINESAGE":
      SageAdapter: $(SageAdapter 2>&1 | grep -E '^Version(.*)' | sed 's/Version: //g' | cut -d ' ' -f 1)
      sage: $(sage 2>&1 | grep -E 'Version [0-9]+\.[0-9]+\.[0-9]+')
  END_VERSIONS

Command exit status:
  6

Command output:
  Invalid string parameter value 'Lys-c/p' for parameter 'enzyme' given! Valid values are: 'Arg-C/P,Asp-N,Asp-N/B,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Trypsin,Arg-C,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,leukocyte elastase,proline endopeptidase,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate'. Updating failed!
  Parameters passed to 'SageAdapter' are invalid. To prevent usage of wrong defaults, please update/fix the parameters!