Chymotrypsin/P force in ComentAdapter, not supported by OpenMS

[ypriverol]

Description of the bug

@timosachsenberg I thought this PR OpenMS/OpenMS#7714 added Chymotrypsin/P in OpenMS.

The exit status of the task that caused the workflow execution to fail was: 6

Error executing process > 'NFCORE_QUANTMS:QUANTMS:LFQ:ID:DATABASESEARCHENGINES:SEARCHENGINECOMET (20150708_QE3_UPLC8_DBJ_QC_HELA_39frac_Chymotrypsin_3)'

Caused by:
  Process `NFCORE_QUANTMS:QUANTMS:LFQ:ID:DATABASESEARCHENGINES:SEARCHENGINECOMET (20150708_QE3_UPLC8_DBJ_QC_HELA_39frac_Chymotrypsin_3)` terminated with an error exit status (6)


Command executed:

  CometAdapter \
      -in 20150708_QE3_UPLC8_DBJ_QC_HELA_39frac_Chymotrypsin_3.mzML \
      -out 20150708_QE3_UPLC8_DBJ_QC_HELA_39frac_Chymotrypsin_3_comet.idXML \
      -threads 8 \
      -database "Homo-sapiens-uniprot-reviewed-contam-entrap-decoy-20241105.fasta" \
      -instrument high_res \
      -missed_cleavages 2 \
      -min_peptide_length 6 \
      -max_peptide_length 40 \
      -num_hits 1 \
      -num_enzyme_termini fully \
      -enzyme "Chymotrypsin/P" \
      -isotope_error 0/1 \
      -precursor_charge 2:4 \
      -fixed_modifications 'Carbamidomethyl (C)' \
      -variable_modifications 'Acetyl (Protein N-term)' 'Deamidated (N)' 'Deamidated (Q)' 'Glu->pyro-Glu (N-term E)' 'Gln->pyro-Glu (N-term Q)' 'Oxidation (M)' 'Phospho (S)' 'Phospho (T)' 'Phospho (Y)' \
      -max_variable_mods_in_peptide 3 \
      -precursor_mass_tolerance 10.0 \
      -precursor_error_units ppm \
      -fragment_mass_tolerance 0.015 \
      -fragment_bin_offset 0.0 \
      -minimum_peaks 10 \
      -PeptideIndexing:IL_equivalent \
      -PeptideIndexing:unmatched_action warn \
      -debug 0 \
      -force \
       \
      2>&1 | tee 20150708_QE3_UPLC8_DBJ_QC_HELA_39frac_Chymotrypsin_3_comet.log
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_QUANTMS:QUANTMS:LFQ:ID:DATABASESEARCHENGINES:SEARCHENGINECOMET":
      CometAdapter: $(CometAdapter 2>&1 | grep -E '^Version(.*)' | sed 's/Version: //g' | cut -d ' ' -f 1)
      Comet: $(comet 2>&1 | grep -E "Comet version.*" | sed 's/ Comet version //g' | sed 's/"//g')
  END_VERSIONS

Command exit status:
  6

Command output:
  Invalid string parameter value 'Chymotrypsin/P' for parameter 'enzyme' given! Valid values are: 'Lys-C,Lys-N,Chymotrypsin,CNBr,unspecific cleavage,Arg-C/P,Asp-N,Trypsin,Arg-C,Lys-C/P,PepsinA,Trypsin/P,leukocyte elastase,glutamyl endopeptidase,no cleavage'. Updating failed!
  Parameters passed to 'CometAdapter' are invalid. To prevent usage of wrong defaults, please update/fix the parameters!

Command wrapper:
  Invalid string parameter value 'Chymotrypsin/P' for parameter 'enzyme' given! Valid values are: 'Lys-C,Lys-N,Chymotrypsin,CNBr,unspecific cleavage,Arg-C/P,Asp-N,Trypsin,Arg-C,Lys-C/P,PepsinA,Trypsin/P,leukocyte elastase,glutamyl endopeptidase,no cleavage'. Updating failed!
  Parameters passed to 'CometAdapter' are invalid. To prevent usage of wrong defaults, please update/fix the parameters!

Work dir:
  /hps/nobackup/juan/pride/reanalysis/absolute-expression/cell-lines/PXD004452/work/9e/50c7621adb58fce5f479b4aec26a1b

Container:
  /hps/nobackup/juan/pride/reanalysis/singularity/ghcr.io-openms-openms-tools-thirdparty-sif-latest.img

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

Command used and terminal output

No response

Relevant files

No response

System information

No response

[ypriverol]

OpenMS/OpenMS#7787