Commit daacdefc authored by Jerome Mariette's avatar Jerome Mariette
Browse files

some updates on r454_diversity

parent 29b205e1
......@@ -20,8 +20,9 @@ class MothurSffinfo(Component):
:param sff_files: a sff file to process
:type sff_files: str
"""
# define input files
self.sff_files = InputFileList(sff_files, Formats.SFF)
# generates 3 output files: fasta, qual and flow
# define output files
self.fasta_files = OutputFileList(self.get_outputs('{basename_woext}.fasta', self.sff_files), Formats.FASTA)
self.qual_files = OutputFileList(self.get_outputs('{basename_woext}.qual', self.sff_files), Formats.QUAL)
self.flow_files = OutputFileList(self.get_outputs('{basename_woext}.flow', self.sff_files), Formats.FLOW)
......
......@@ -21,8 +21,11 @@ class MothurShhhFlows(Component):
:param processors: the number of processors to use
:type processors: int
"""
# define parameters
self.processors = processors
# define input files
self.flow_files = InputFileList(flow_files, Formats.FLOW)
# define output files
self.qual_files = OutputFileList(self.get_outputs('{basename_woext}.shhh.qual', self.flow_files), Formats.QUAL)
self.fasta_files = OutputFileList(self.get_outputs('{basename_woext}.shhh.fasta', self.flow_files), Formats.FASTA)
self.names_files = OutputFileList(self.get_outputs('{basename_woext}.shhh.names', self.flow_files), Formats.MOTHUR_NAMES)
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment