nf-test
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support for loading multiline strings in yaml params files
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 {
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