Commit 4ed31b07 authored by Jerome Mariette's avatar Jerome Mariette
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parent cd66b796
......@@ -42,17 +42,15 @@ class RNAdiversity (Workflow):
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])
#summaryseqs_screen = self.add_component("MothurSummarySeqs", [screenseqs.good_align_files,screenseqs.good_names_files],{},"screen")
#filterseqs = self.add_component("MothurFilterSeqs",[screenseqs.good_align_files])
#uniqueseqs_filter = self.add_component("MothurUniqueSeqs",[filterseqs.filter_fasta_files,screenseqs.good_names_files],{},"filter")
#precluster = self.add_component("MothurPreCluster",[uniqueseqs_filter.unique_fasta_files,uniqueseqs_filter.names_files,screenseqs.good_groups_files])
#summaryseqs_precluster = self.add_component("MothurSummarySeqs", [precluster.precluster_fasta_files,precluster.precluster_names_files],{},"precluster")
#chimerauchime = self.add_component("MothurChimeraUchime",[precluster.precluster_fasta_files,precluster.precluster_names_files,screenseqs.good_groups_files])
#removeseqs = self.add_component("MothurRemoveSeqs",[chimerauchime.uchime_accnos_files,precluster.precluster_fasta_files,precluster.precluster_names_files,\
# screenseqs.good_groups_files])
#summaryseqs_removeseqs = self.add_component("MothurSummarySeqs", [removeseqs.pick_fasta_files,removeseqs.pick_names_files],{},"removeseqs")
#classifyseqs = self.add_component("MothurClassifySeqs",[removeseqs.pick_fasta_files,removeseqs.pick_names_files,removeseqs.pick_groups_files,self.args["template"],\
# self.args["taxonomy"]])
# removegroups = self.add_component("MothurRemoveGroups", [removeseqs.pick_fasta_files,removeseqs.pick_names_files,removeseqs.pick_groups_files,classifyseqs.taxonomy_files])
......
......@@ -27,7 +27,7 @@ class MothurSummarySeqs(Component):
if names_files:
self.names_files = InputFileList(self.names_files, Formats.MOTHUR_NAMES)
#define output files
self.summary_files = OutputFileList(self.get_outputs('{basename_woext}.summary', self.fasta_files), Formats.MOTHUR_SUMMARY)
self.summary_files = OutputFileList(self.get_outputs('{basename_woext}.summary', self.fasta_files))
self.stdout = OutputFileList(self.get_outputs('{basename_woext}.stdout', self.fasta_files))
def process(self):
......
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