Error fixed: file not found: 'MSGFPlus.jar' in google cloud

[kdommaraju]

Description of the bug

Error executing process > 'NFCORE_QUANTMS:QUANTMS:LFQ:ID:DATABASESEARCHENGINES:SEARCHENGINEMSGF (BSA2_F2)'

Caused by:
Process NFCORE_QUANTMS:QUANTMS:LFQ:ID:DATABASESEARCHENGINES:SEARCHENGINEMSGF (BSA2_F2) terminated with an error exit status (1)

Command executed:

MSGFPlusAdapter
-protocol automatic
-in BSA2_F2.mzML
-out BSA2_F2_msgf.idXML

-threads 2
-java_memory 6144 \
-database "18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta"
-instrument high_res
-matches_per_spec 1
-min_precursor_charge 2
-max_precursor_charge 4
-min_peptide_length 6
-max_peptide_length 40
-max_missed_cleavages 2
-isotope_error_range 0,1
-enzyme "Trypsin/P"
-tryptic fully
-precursor_mass_tolerance 5
-precursor_error_units ppm
-fixed_modifications 'Carbamidomethyl (C)'
-variable_modifications 'Oxidation (M)'
-max_mods 3
-PeptideIndexing:IL_equivalent
-PeptideIndexing:unmatched_action warn
-debug 0

2>&1 | tee BSA2_F2_msgf.log

cat <<-END_VERSIONS > versions.yml
"NFCORE_QUANTMS:QUANTMS:LFQ:ID:DATABASESEARCHENGINES:SEARCHENGINEMSGF":
MSGFPlusAdapter: $(MSGFPlusAdapter 2>&1 | grep -E '^Version(.)' | sed 's/Version: //g' | cut -d ' ' -f 1)
msgf_plus: $(msgf_plus 2>&1 | grep -E '^MS-GF+ Release.')
END_VERSIONS

Command exit status:
1

Command output:
Input file 'MSGFPlus.jar' could not be found (by searching on PATH). Either provide a full filepath or fix your PATH environment!
Error: File not found (the file 'MSGFPlus.jar' could not be found)

Command used and terminal output

No response

Relevant files

No response

System information

No response

[kdommaraju]

Added google-lifesciences in the executor list fixed the following error

Error: File not found (the file 'MSGFPlus.jar' could not be found)

if ((workflow.containerEngine || (task.executor == "awsbatch") || (task.executor == google-lifesciences’))