Commit 030fcd9c authored by Penom Nom's avatar Penom Nom
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parent a86bbaa4
......@@ -105,10 +105,10 @@ class IlluminaRNAdiversity (NG6Workflow):
if fileExtension == fileFormat:
gunzip = self.add_component("GunZipFiles",[concat_read1_files,concat_read2_files])
makecontigs = self.add_component("MothurMakeContigs", kwargs={'read1_files':gunzip.fastq_R1,'read2_files':gunzip.fastq_R2,\
'sample_name': self.args["sample_name"],'maxambig':'0','maxlength':self.args["length_contigs"]}, parent=fastqilluminafilter)
'sample_name': self.args["sample_name"],'maxambig':'0','maxlength':self.args["length_contigs"]}, component_prefix="test", parent=fastqilluminafilter)
else:
makecontigs = self.add_component("MothurMakeContigs", kwargs={'read1_files':concat_read1_files,'read2_files':concat_read2_files,\
'sample_name': self.args["sample_name"],'maxambig':'0','maxlength':self.args["length_contigs"]}, parent=fastqilluminafilter)
'sample_name': self.args["sample_name"],'maxambig':'0','maxlength':self.args["length_contigs"]}, parent=fastqilluminafilter)
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"],\
......
......@@ -26,9 +26,9 @@ class RNAdiversity (NG6Workflow):
trim_fasta = self.add_component("MothurTrimSeqs", kwargs={'fasta_files':sff_pre_treatment.shhh_fasta_files,'names_files':sff_pre_treatment.names_files,\
'groups_files':sff_pre_treatment.groups_files,'forward_primer':self.args["forward_primer"],'reverse_primer':self.args["reverse_primer"],'sample_barcodes':self.args["sample_barcodes"]}\
,parent = sff_pre_treatment)
# elif self.args["input_files"].endswith('.fasta'):
# trim_fasta = self.add_component("MothurTrimSeqs", kwargs={'fasta_files':self.args["input_files"],'forward_primer':self.args["forward_primer"],\
# 'reverse_primer':self.args["reverse_primer"]}, component_prefix="fasta")
elif self.args["input_files"].endswith('.fasta'):
trim_fasta = self.add_component("MothurTrimSeqs", kwargs={'fasta_files':self.args["input_files"],'forward_primer':self.args["forward_primer"],\
'reverse_primer':self.args["reverse_primer"]}, component_prefix="fasta")
uniqueseqs = self.add_component("MothurUniqueSeqs", [trim_fasta.p_trim_fasta_files, trim_fasta.p_trim_names_files])
alignseqs = self.add_component("MothurAlign", kwargs={'fasta_files':uniqueseqs.unique_fasta_files,'reference_alignment_files':self.args["reference_alignment"],\
'names_files':uniqueseqs.unique_names_files,'groups_files':trim_fasta.p_groups_files},parent = trim_fasta)
......
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