diff --git a/workflow/scripts/check_design.py b/workflow/scripts/check_design.py index 161660e03979faee3561808b130f1e4ea0fa1c31..6bd822f3334a65fef86f6e953edb6538e45a4d64 100644 --- a/workflow/scripts/check_design.py +++ b/workflow/scripts/check_design.py @@ -21,6 +21,7 @@ logger.setLevel(logging.INFO) def get_args(): '''Define arguments.''' + parser = argparse.ArgumentParser( description=__doc__, epilog=EPILOG, formatter_class=argparse.RawDescriptionHelpFormatter) @@ -98,7 +99,7 @@ def check_replicates(design): unique_replicates = set(replicates) if len(replicates) != len(unique_replicates): duplicated_replicates.append(experiment) - + if len(duplicated_replicates) > 0: logger.error('Duplicate replicates in experiments: %s', list(duplicated_replicates)) raise Exception("Duplicate replicates in experiments: %s" % diff --git a/workflow/scripts/convert_reads.py b/workflow/scripts/convert_reads.py index d7450475c5be71023c365aa6dfecfd3ddb0ddc7e..62faf7258291ae63ff4eab0dd02ee7bb6ff1fa12 100644 --- a/workflow/scripts/convert_reads.py +++ b/workflow/scripts/convert_reads.py @@ -25,6 +25,7 @@ logger.setLevel(logging.INFO) def get_args(): '''Define arguments.''' + parser = argparse.ArgumentParser( description=__doc__, epilog=EPILOG, formatter_class=argparse.RawDescriptionHelpFormatter) diff --git a/workflow/scripts/experiment_design.py b/workflow/scripts/experiment_design.py index ca135e8ec53bf0fc4d651192ca3645b57a975003..3d6697a9adb11b0caf7df47627aeebd472fdb77f 100644 --- a/workflow/scripts/experiment_design.py +++ b/workflow/scripts/experiment_design.py @@ -21,6 +21,7 @@ logger.setLevel(logging.INFO) def get_args(): '''Define arguments.''' + parser = argparse.ArgumentParser( description=__doc__, epilog=EPILOG, formatter_class=argparse.RawDescriptionHelpFormatter) diff --git a/workflow/scripts/experiment_qc.py b/workflow/scripts/experiment_qc.py index 47a398344fa789fb2a5c5abf159db5375b500efe..711da1888ab9045b361b9c877dd99b7fe09e37f6 100644 --- a/workflow/scripts/experiment_qc.py +++ b/workflow/scripts/experiment_qc.py @@ -25,6 +25,7 @@ logger.setLevel(logging.INFO) def get_args(): '''Define arguments.''' + parser = argparse.ArgumentParser( description=__doc__, epilog=EPILOG, formatter_class=argparse.RawDescriptionHelpFormatter) diff --git a/workflow/scripts/map_qc.py b/workflow/scripts/map_qc.py index 4451d916126fce6d4683539005a9cdda89c3f50a..3f07068352724bfd86f7513342e373fc4fabc779 100644 --- a/workflow/scripts/map_qc.py +++ b/workflow/scripts/map_qc.py @@ -34,6 +34,7 @@ STRIP_EXTENSIONS = ['.bam', '.srt'] def get_args(): '''Define arguments.''' + parser = argparse.ArgumentParser( description=__doc__, epilog=EPILOG, formatter_class=argparse.RawDescriptionHelpFormatter) diff --git a/workflow/scripts/map_reads.py b/workflow/scripts/map_reads.py index ba6bbd0722a49ab09ddd84befbfe0a0ce3e07f19..b7d3144fe8484f2d8939c773229c45b58e283315 100644 --- a/workflow/scripts/map_reads.py +++ b/workflow/scripts/map_reads.py @@ -33,6 +33,7 @@ STRIP_EXTENSIONS = ['.gz', '.fq', '.fastq', '_trimmed'] def get_args(): '''Define arguments.''' + parser = argparse.ArgumentParser( description=__doc__, epilog=EPILOG, formatter_class=argparse.RawDescriptionHelpFormatter) diff --git a/workflow/scripts/trim_reads.py b/workflow/scripts/trim_reads.py index f9f2524f942fb356c360696cee70ea80a403cc4b..2f7f3e557299bf02cf5ac9f315e4e335d962fec8 100644 --- a/workflow/scripts/trim_reads.py +++ b/workflow/scripts/trim_reads.py @@ -22,6 +22,7 @@ logger.setLevel(logging.INFO) def get_args(): '''Define arguments.''' + parser = argparse.ArgumentParser( description=__doc__, epilog=EPILOG, formatter_class=argparse.RawDescriptionHelpFormatter) diff --git a/workflow/scripts/xcor.py b/workflow/scripts/xcor.py index 88750b6d5e5e128ff7b9a2faf843f0eb165bfd5b..0bf51e6400d05d2ea9cdb978883fed3c765d3100 100644 --- a/workflow/scripts/xcor.py +++ b/workflow/scripts/xcor.py @@ -24,6 +24,7 @@ logger.setLevel(logging.INFO) def get_args(): '''Define arguments.''' + parser = argparse.ArgumentParser( description=__doc__, epilog=EPILOG, formatter_class=argparse.RawDescriptionHelpFormatter)