Commit f132321d authored by Claire Kuchly's avatar Claire Kuchly
Browse files

new cutadapt ligne

parent 2b9a3507
......@@ -101,16 +101,16 @@ class IlluminaMatePair (NG6Workflow):
contamination_search = self.add_component("ContaminationSearch", [filtered_read1_files+filtered_read2_files, self.args["databank"], reads_prefixes], parent = fastqilluminafilter)
# mate_pair analyse
cutadapt = self.add_component("CutAdapt",[filtered_read1_files,filtered_read2_files,{"a":["CTGTCTCTTATACACATCT","AGATCTATAAGAGACAG"]},{"a":["CTGTCTCTTATACACATCT","AGATCTATAAGAGACAG"]},is_paired_end,0.1,20 ],parent= fastqilluminafilter)
cutadapt = self.add_component("CutAdapt",[filtered_read1_files,filtered_read2_files,{"g":["CTGTCTCTT","ATACACATCT","AGATCTAT","AAGAGACAG"]},{"g":["CTGTCTCTT","ATACACATCT","AGATCTAT","AAGAGACAG"]},is_paired_end,0.1,4,20 ],parent= fastqilluminafilter)
#reverse_complement
revcom1 = self.add_component("FastxReverseComplement",cutadapt.output_files_R1,component_prefix="read1")
revcom2 = self.add_component("FastxReverseComplement",cutadapt.output_files_R2,component_prefix="read2")
revcom1 = self.add_component("FastxReverseComplement",[cutadapt.output_files_R1],component_prefix="read1")
revcom2 = self.add_component("FastxReverseComplement",[cutadapt.output_files_R2],component_prefix="read2")
# make some statistics on filtered file
fastqc = self.add_component("FastQC", [revcom1.output_files+revcom2.output_files, (group_prefix is not None), True, run_name+"_fastqc.tar.gz"], parent = cutadapt, component_prefix="Trimmed_read")
#gunzip = self.add_component("GunZipFiles",revcom1.output_files, revcom2.output_files)
if self.args["reference_genome"]:
# index the reference genome if not already indexed
......
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