Commit f2c99462 authored by khalid's avatar khalid
Browse files

debug fastp

parent 14182ee0
......@@ -13,9 +13,9 @@ if config["SeOrPe"] == "PE":
complexity_threshold = config["<step_name>__fastp_complexity_threshold"],
report_title = config["<step_name>__fastp_report_title"],
detect_adapter_for_pe = "--detect_adapter_for_pe" if config["<step_name>__fastp_adapter_detection_PE"] == True else "",
adapter_sequence = config["<step_name>__fastp_adapter_sequence"],
adapter_sequence_R2 = config["<step_name>__fastp_adapter_sequence_R2_PE"],
P = config["<step_name>__fastp_P_PE"],
adapter_sequence = "--adapter_sequence "+config["<step_name>__fastp_adapter_sequence"] if config["<step_name>__fastp_adapter_sequence"] != "" else "",
adapter_sequence_R2 = "--adapter_sequence_r2 " + config["<step_name>__fastp_adapter_sequence_R2_PE"] if config["<step_name>__fastp_adapter_sequence_R2_PE"] != "" else "",
P = "-P" + config["<step_name>__fastp_P_PE"] if config["<step_name>__fastp_overrepresentation_analysis"] == True else "",
output_dir = config["<step_name>__fastp_PE_output_dir"],
correction = "--correction " if config["<step_name>__fastp_correction_PE"] == True else "",
low_complexity_filter = "--low_complexity_filter " if config["<step_name>__fastp_low_complexity_filter"] == True else "",
......@@ -38,10 +38,10 @@ if config["SeOrPe"] == "PE":
"--json {output.report_json} "
"--report_title {params.report_title} "
"{params.detect_adapter_for_pe} "
"--adapter_sequence '{params.adapter_sequence}' "
"--adapter_sequence_r2 '{params.adapter_sequence_R2}' "
"{params.adapter_sequence} "
"{params.adapter_sequence_R2} "
"{params.overrepresentation_analysis} "
"-P {params.P} "
"{params.P} "
"|& tee {log}"
......
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