Commit 122e9fbf authored by Jerome Mariette's avatar Jerome Mariette
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parent 4ed31b07
......@@ -38,10 +38,10 @@ class RNAdiversity (Workflow):
# then process the workflow
sffinfo = self.add_component("MothurSffinfo", [self.args["sff_files"]])
shhhflows = self.add_component("MothurShhhFlows",[sffinfo.flow_files])
trimseqs = self.add_component("MothurTrimSeqs",[shhhflows.fasta_files, oligos_fullpath, shhhflows.names_files])
uniqueseqs = self.add_component("MothurUniqueSeqs",[trimseqs.trim_fasta_files, trimseqs.trim_names_files])
alignseqs = self.add_component("MothurAlignSeqs",[uniqueseqs.unique_fasta_files,self.args["reference_alignment"]])
shhhflows = self.add_component("MothurShhhFlows", [sffinfo.flow_files])
trimseqs = self.add_component("MothurTrimSeqs", [shhhflows.fasta_files, oligos_fullpath, shhhflows.names_files])
uniqueseqs = self.add_component("MothurUniqueSeqs", [trimseqs.trim_fasta_files, trimseqs.trim_names_files])
alignseqs = self.add_component("MothurAlignSeqs", [uniqueseqs.unique_fasta_files,self.args["reference_alignment"]])
summaryseqs_align = self.add_component("MothurSummarySeqs", [alignseqs.align_files,uniqueseqs.unique_names_files],component_prefix="align")
#screenseqs = self.add_component("MothurScreenSeqs",[alignseqs.align_files,uniqueseqs.names_files,trimseqs.groups_files])
......
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