Commit 7b007b3b authored by ckuchly's avatar ckuchly
Browse files

Initial changes to fetch to Sequel2 parameters

parent 6936ef19
......@@ -31,8 +31,8 @@ class SequelQualityCheck (NG6Workflow):
def define_parameters(self, function="process"):
logging.getLogger("jflow").debug("SequelQC | SequelQualityCheck.define_parameters!")
self.add_parameter("nb_threads", "Number of threads to use for fastqc. Each thread will be allocated 250MB of memory.", default=3)
self.add_parameter("min_subreads_length", "Subreads shorter than this value (in base pairs) are filtered out and excluded from analysis", default=0, type='int')
self.add_parameter("CCS_min_reads_length", "Subreads shorter than this value (in base pairs) are filtered out and excluded from CCS analysis", default=0, type='int')
self.add_parameter("CCS_min_passes", "Minimum of passes for CSS analys ", default=3, type='int')
self.add_parameter("polymerase_read_qual", "Polymerase reads with lower quality than this value are filtered out and excluded from analysis", default=0, type='float')
self.add_parameter("polymerase_read_length", "Polymerase reads shorter than this value (in base pairs) are filtered out and excluded from analysis", default=0, type='int')
......@@ -47,9 +47,9 @@ class SequelQualityCheck (NG6Workflow):
sample_names.append( sample.name )
infiles.append(sample.reads1[0])
add_pacbio_raw_file = self.add_component("AddPacBioRawFiles", [self.runobj, self.get_all_reads()])
h5tofastq = self.add_component("H5toFastq", [sample_names, infiles])
fastqc = self.add_component("FastQC", [h5tofastq.output_fastqs, False, False, "fastqc.tar.gz", self.nb_threads], parent = h5tofastq)
self.add_component("RS_Subreads", [sample_names, infiles,self.min_subreads_length,self.polymerase_read_qual,self.polymerase_read_length,self.barcode_file,self.barcode_score ])
#h5tofastq = self.add_component("H5toFastq", [sample_names, infiles])
#fastqc = self.add_component("FastQC", [h5tofastq.output_fastqs, False, False, "fastqc.tar.gz", self.nb_threads], parent = h5tofastq)
#self.add_component("RS_Subreads", [sample_names, infiles,self.min_subreads_length,self.polymerase_read_qual,self.polymerase_read_length,self.barcode_file,self.barcode_score ])
logging.getLogger("jflow").debug("SequelQC | SequelQualityCheck.process ended!")
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