Commit 41883883 authored by bow's avatar bow
Browse files

Add all fastqc plots to report

parent 3c2f3b45
......@@ -389,21 +389,17 @@ class GentrapLib(object):
self.trimming = not self.flexiprep["settings"]["skip_trim"]
self.is_paired_end = self.flexiprep["settings"]["paired"]
if "fastqc_R1" in self.flexiprep["files"]:
self.fastqc_r1 = FastQC(self.flexiprep["files"]["fastqc_R1"]["fastqc_data"]["path"])
else:
self.fastqc_r1 = None
self.fastqc_r1_files = self.flexiprep["files"]["fastqc_R1"]
self.fastqc_r1 = FastQC(self.fastqc_r1_files["fastqc_data"]["path"])
if "fastqc_R2" in self.flexiprep["files"]:
self.fastqc_r2 = FastQC(self.flexiprep["files"]["fastqc_R2"]["fastqc_data"]["path"])
else:
self.fastqc_r2 = None
self.fastqc_r2_files = self.flexiprep["files"]["fastqc_R2"]
self.fastqc_r2 = FastQC(self.fastqc_r2_files["fastqc_data"]["path"])
if "fastqc_R1_qc" in self.flexiprep["files"]:
self.fastqc_r1_qc = FastQC(self.flexiprep["files"]["fastqc_R1_qc"]["fastqc_data"]["path"])
else:
self.fastqc_r1_qc = None
self.fastqc_r1_qc_files = self.flexiprep["files"]["fastqc_R1_qc"]
self.fastqc_r1_qc = FastQC(self.fastqc_r1_qc_files["fastqc_data"]["path"])
if "fastqc_R2_qc" in self.flexiprep["files"]:
self.fastqc_r2_qc = FastQC(self.flexiprep["files"]["fastqc_R2_qc"]["fastqc_data"]["path"])
else:
self.fastqc_r2_qc = None
self.fastqc_r2_qc_files = self.flexiprep["files"]["fastqc_R2_qc"]
self.fastqc_r2_qc = FastQC(self.fastqc_r2_qc_files["fastqc_data"]["path"])
def __repr__(self):
return "{0}(sample=\"{1}\", lib=\"{2}\")".format(
......
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