Commit 9bfb3a76 authored by Maxime Manno's avatar Maxime Manno 🍜
Browse files

Change default archive name

parent b3a4e2c3
......@@ -29,12 +29,12 @@ class Trim_porechop (Analysis):
This module trim the reads from ONT data
"""
def define_parameters(self, fastq_files, nbthreads, formatfile, discard_middle, archivename):
def define_parameters(self, fastq_files, nbthreads, formatfile, discard_middle, archivename="porechop_archive"):
self.add_input_file_list( "fastq_files", "fastq_files", default=fastq_files, required=True, file_format = 'fastq')
self.add_parameter("nbthreads", "number of threads to use (default=16)", default=16, type='int')
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="porechop_archive", type='str')
self.add_parameter("archive_name", "Name of the archive", default=archivename, type='str')
output_ext = '_trim.'+self.formatfile
self.add_output_file_list( "files_trimmed", "files_trimmed", pattern='{basename_woext}' + output_ext, items=self.fastq_files, file_format = self.formatfile)
self.add_output_file_list("stdouts", "stdouts", pattern='{basename_woext}.stdout', items=self.fastq_files)
......
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