diff --git a/atlas/make_config.py b/atlas/make_config.py index 96332497..e65025b7 100644 --- a/atlas/make_config.py +++ b/atlas/make_config.py @@ -21,9 +21,9 @@ def make_default_config(): config["simplejob_mem"] = 10 config["simplejob_threads"] = 4 - config[ - "importqc_params" - ] = "iupacToN=t touppercase=t qout=33 addslash=t trimreaddescription=t" + config["importqc_params"] = ( + "iupacToN=t touppercase=t qout=33 addslash=t trimreaddescription=t" + ) config["mem"] = MEM config["large_mem"] = 250 diff --git a/workflow/report/bin_report.py b/workflow/report/bin_report.py index dc308b3b..c2918139 100644 --- a/workflow/report/bin_report.py +++ b/workflow/report/bin_report.py @@ -68,9 +68,9 @@ def add_stats(name, d): add_stats("All", df) df.eval("Quality_score = Completeness - 5* Contamination", inplace=True) - div[ - "QualityScore" - ] = "
Quality score is calculated as: Completeness - 5 x Contamination.
" + div["QualityScore"] = ( + "Quality score is calculated as: Completeness - 5 x Contamination.
" + ) add_stats("Quality score >50 ", df.query("Quality_score>50")) add_stats("Good quality", df.query("Completeness>90 & Contamination <5")) add_stats("Quality score >90 ", df.query("Quality_score>90")) diff --git a/workflow/report/qc_report.py b/workflow/report/qc_report.py index a5342749..dbc132cf 100644 --- a/workflow/report/qc_report.py +++ b/workflow/report/qc_report.py @@ -236,9 +236,9 @@ def make_plots( ### Insert insert_size_stats if insert_size_stats is None: - div[ - "Insert" - ] = "Insert size information is not available for single end reads.
" + div["Insert"] = ( + "Insert size information is not available for single end reads.
" + ) else: data_insert = pd.read_table(insert_size_stats, index_col=0) data_insert.index.name = "Sample"