Commit 02abb6e8 authored by mmanno's avatar mmanno
Browse files

ONT-QC : by default, no timming for gridion and promethion

parent a41a3010
...@@ -30,7 +30,7 @@ class OntQualityCheck (NG6Workflow): ...@@ -30,7 +30,7 @@ class OntQualityCheck (NG6Workflow):
def define_parameters(self, function="process"): def define_parameters(self, function="process"):
logging.getLogger("jflow").debug("Begin OntQualityCheck.define_parameters! ont_qc") logging.getLogger("jflow").debug("Begin OntQualityCheck.define_parameters! ont_qc")
self.add_parameter("compression", "How should the data be compressed once archived", choices= [ "none", "gz", "bz2"], default = "gz") self.add_parameter("compression", "How should the data be compressed once archived", choices= [ "none", "gz", "bz2"], default = "gz")
self.add_parameter("trimming", "use trimming with porechop or not",choices= [ "yes", "no"], default = "yes") self.add_parameter("trimming", "use trimming with porechop or not",choices= [ "yes", "no"], default = "no")
self.add_parameter("nb_threads", "Number of threads to use for porechop (default=16).", default=16) self.add_parameter("nb_threads", "Number of threads to use for porechop (default=16).", default=16)
self.add_parameter("fileformat", "The file format for porechop (default=fastq).", choices= [ "fastq", "fasta"], default = "fastq") self.add_parameter("fileformat", "The file format for porechop (default=fastq).", choices= [ "fastq", "fasta"], default = "fastq")
self.add_input_file( "summary_file", "Input summary basecalling file", default=None) self.add_input_file( "summary_file", "Input summary basecalling file", default=None)
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