Commit b1d217d4 authored by Penom Nom's avatar Penom Nom
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parent ca58357f
......@@ -91,9 +91,9 @@ class Methylseq (CasavaNG6Workflow):
trim_galore = self.add_component("TrimGalore", [ concat_read1_files, concat_read2_files, self.non_directional, self.rrbs], parent = fastqilluminafilter)
# make some statistics on cleaned files
fastq_cleaned = trim_galore.output_files_R1
if self.is_paired_end():
fastq_cleaned = trim_galore.output_files_R1 + trim_galore.output_files_R2
fastqcCleaned = self.add_component("FastQC", [fastq_cleaned, (self.group_prefix is not None), True, run_name+"_trim_galore_fastqc.tar.gz"], component_prefix="trim_galore", parent = trim_galore)
#Alignement against the reference genome
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