Commit 0fa6fe43 authored by Jerome Mariette's avatar Jerome Mariette
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parent 55900cc1
......@@ -129,14 +129,17 @@ class MiSeqDiversity (NG6Workflow):
uniqueseqs = self.add_component("MothurUniqueSeqs", [makecontigs.good_fasta_files])
countseqs = self.add_component("MothurCountSeqs", [uniqueseqs.unique_names_files,makecontigs.good_groups_files])
pcrseqs = self.add_component("MothurPcrSeqs",
kwargs={'fasta_files':self.args["reference_alignment"],
'forward_primer':self.args["forward_primer"],
'reverse_primer':self.args["reverse_primer"]})
alignment_template = self.args["reference_alignment"]
if self.args["trunk_ref"]:
pcrseqs = self.add_component("MothurPcrSeqs",
kwargs={'fasta_files':self.args["reference_alignment"],
'forward_primer':self.args["forward_primer"],
'reverse_primer':self.args["reverse_primer"]})
alignment_template = pcrseqs.pcr_fasta_files
alignseqs = self.add_component("MothurAlign",
kwargs={'fasta_files':uniqueseqs.unique_fasta_files,
'reference_alignment_files':pcrseqs.pcr_fasta_files,
'reference_alignment_files':alignment_template,
'count_table_files':countseqs.count_table_files,
'maxhomop':self.args["max_homopolymers"],
'processors':self.args["processors"]},
......
......@@ -134,3 +134,8 @@ without_krona.flag = --without-krona
without_krona.type = bool
without_krona.default = False
without_krona.help = Should krona figures be computed (can be time consuming)
trunk_ref.flag = --trunk-ref
trunk_ref.type = bool
trunk_ref.default = False
trunk_ref.help = Should the reference be truncated
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