Commit b64f0e15 authored by Maxime Manno's avatar Maxime Manno 🍜
Browse files

ONT - remove format file parameter

parent 408197ff
......@@ -31,7 +31,6 @@ class OntQualityCheck (NG6Workflow):
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("trimming", "use trimming with porechop or not",choices= [ "yes", "no"], default = "no")
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_parameter("barcoded", "Barcoded run or not", choices= [ "yes", "no"], default = "no")
self.add_parameter("fast5dir", "path of the fast5 directory", default = None)
......@@ -53,7 +52,7 @@ class OntQualityCheck (NG6Workflow):
#nanoplot = self.add_component("Nanoplot", [,self.get_all_reads(), self.nb_threads, True, "png", self.nanoplot_color,"nanoplot.tar.gz"])
ontstat = self.add_component("Run_stats", [self.summary_file, self.barcoded])
if self.trimming == "yes":
trim_porechop = self.add_component("Trim_porechop", [self.get_all_reads(), self.fileformat , "discard_middle"])
trim_porechop = self.add_component("Trim_porechop", [self.get_all_reads() , "discard_middle"])
if self.fast5dir != None:
fast5archive = self.add_component("Fast5archive", [self.fast5dir, "fast5archive.tar"])
......@@ -31,7 +31,6 @@ class Trim_porechop (Analysis):
def define_parameters(self, fastq_files, nbthreads, formatfile, discard_middle, archivename="porechop_archive.tar"):
self.add_input_file_list( "fastq_files", "fastq_files", default=fastq_files, required=True, file_format = 'fastq')
self.add_parameter("formatfile", "format of the input files", default="fastq", type='str')
self.add_parameter("discard_middle", "discard_middle", default="discard_middle", choices=[ "discard_middle", "do_not_discard_middle"])
self.add_parameter("archive_name", "Name of the archive", default=archivename, type='str')
output_ext = '_trim.'+self.formatfile
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