Open seanrjohnson opened 2 months ago
For pipeline tests, the params load config file function parses multiline strings in yml files differently than supplying them to nextFlow via the command line -params-file option.
-params-file
params { load("example_params.yml") }
Json file parsed correctly:
{ "query_sequence": ">A0A2G2JID1\nMPIAQIHILEGRSDEQKETLIREVSEAISRSLDAPLTSVRVIITEMAKGHFGIGGELASKVRR\n>A0A8G5FSM5\nMPIAQLYILEGRSDEQKESLIREISEAMSRSLDAPIERVRVIITEMPKNHFGIGGEPASKLNR\n>A0A0F9USC8\nMPIAQLHILEGRTDEQKEALIREVSEAIARALDAPMPSIRVIISEMPKAHFGIGGEPASKVRR\n>A0A3S8ND41\nMPVAQINILEGRSDEQKETLIREVSEAISRSLGAPVENVRIIITEMPKQHFGIGGQSAKKRGR\n", "query_file": null, "identity": 100, "fasta_type": "protein", "algorithm": "cd-hit", "output_type": "genbank", "count": "prefix" }
.yml file not parsed correctly (deletes newlines in "query_sequence"):
query_sequence: ">A0A2G2JID1\nMPIAQIHILEGRSDEQKETLIREVSEAISRSLDAPLTSVRVIITEMAKGHFGIGGELASKVRR\n>A0A8G5FSM5\nMPIAQLYILEGRSDEQKESLIREISEAMSRSLDAPIERVRVIITEMPKNHFGIGGEPASKLNR\n>A0A0F9USC8\nMPIAQLHILEGRTDEQKEALIREVSEAIARALDAPMPSIRVIISEMPKAHFGIGGEPASKVRR\n>A0A3S8ND41\nMPVAQINILEGRSDEQKETLIREVSEAISRSLGAPVENVRIIITEMPKQHFGIGGQSAKKRGR\n" query_file: identity: 100 fasta_type: protein algorithm: cd-hit output_type: genbank count: prefix
.yml file also not parsed correctly (deletes newlines in "query_sequence"):
query_sequence: | >A0A2G2JID1 MPIAQIHILEGRSDEQKETLIREVSEAISRSLDAPLTSVRVIITEMAKGHFGIGGELASKVRR >A0A8G5FSM5 MPIAQLYILEGRSDEQKESLIREISEAMSRSLDAPIERVRVIITEMPKNHFGIGGEPASKLNR >A0A0F9USC8 MPIAQLHILEGRTDEQKEALIREVSEAIARALDAPMPSIRVIISEMPKAHFGIGGEPASKVRR >A0A3S8ND41 MPVAQINILEGRSDEQKETLIREVSEAISRSLGAPVENVRIIITEMPKQHFGIGGQSAKKRGR query_file: identity: 100 fasta_type: protein algorithm: cd-hit output_type: genbank count: prefix
For pipeline tests, the params load config file function parses multiline strings in yml files differently than supplying them to nextFlow via the command line
-params-file
option.Json file parsed correctly:
.yml file not parsed correctly (deletes newlines in "query_sequence"):
.yml file also not parsed correctly (deletes newlines in "query_sequence"):