Commit fcba0eef authored by Penom Nom's avatar Penom Nom
Browse files

Correction of fileformat

parent 66af0576
......@@ -30,8 +30,8 @@ class SFFExtractA (Analysis):
def define_parameters(self, input_files, archive_name=None):
self.add_input_file_list( "input_files", "input sff files", default=input_files, required=True, file_format = sff)
self.add_parameter("archive_name", "Archive name", default=archive_name)
self.add_output_file_list( "fastq_files", "Outputed fastq files.", pattern='{basename_woext}.fastq', items=input_files, file_format=fastq)
self.add_output_file_list( "stdouts", "SFFExtractA stdout files.", pattern='{basename_woext}.stdout', items=input_files)
self.add_output_file_list( "fastq_files", "Outputed fastq files.", pattern='{basename_woext}.fastq', items=self.input_files, file_format='fastq')
self.add_output_file_list( "stdouts", "SFFExtractA stdout files.", pattern='{basename_woext}.stdout', items=self.input_files)
def define_analysis(self):
self.name = "Convert"
......
......@@ -22,18 +22,16 @@ from ng6.analysis import Analysis
from weaver.function import ShellFunction
from workflows.formats import sff
class SFFfile (Analysis):
def define_parameters(self, sff_file, files_prefix, midscheme, mids_config_file):
files_prefix = os.path.join(self.output_directory, files_prefix)
self.add_input_file("sff_file", "Input sff file", default=sff_file, required=True, file_format = sff)
self.add_input_file("sff_file", "Input sff file", default=sff_file, required=True, file_format = 'sff')
self.add_parameter("files_prefix", "Prefix for output files", default=files_prefix, required=True)
self.add_parameter("midscheme", "midscheme", default=midscheme, required=True)
self.add_input_file("mids_config_file", "mids_config_file path", default=mids_config_file, required=True)
self.add_output_file_endswith( "splited_sffs", "Output sff file", pattern = '.sff', file_format=sff)
self.add_output_file_endswith( "splited_sffs", "Output sff file", pattern = '.sff', file_format='sff')
self.add_output_file( "stdout", "SFFfile stdout", filename=os.path.splitext(os.path.basename(sff_file))[0]+".stdout")
def define_analysis(self):
......
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