45 lines
1.1 KiB
Python
Executable File
45 lines
1.1 KiB
Python
Executable File
#!/usr/bin/env python
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"""Create workflow report."""
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import argparse
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from aplanat.components import fastcat
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from aplanat.report import HTMLReport
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def main():
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"""Run the entry point."""
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parser = argparse.ArgumentParser()
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parser.add_argument("report", help="Report output file")
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parser.add_argument("summaries", nargs='+', help="Read summary file.")
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args = parser.parse_args()
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report = HTMLReport(
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"Workflow Template Sequencing report",
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("Results generated through the wf-template nextflow "
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"workflow by Oxford Nanopore Technologies"))
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report.add_section(
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section=fastcat.full_report(args.summaries))
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report.markdown('''
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### About
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**Oxford Nanopore Technologies products are not intended for use for health
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assessment or to diagnose, treat, mitigate, cure or prevent any disease or
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condition.**
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This report was produced using the
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[epi2me-labs/wf-template](https://github.com/epi2me-labs/wf-template). The
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workflow can be run using `nextflow epi2me-labs/wf-template --help`
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---
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''')
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# write report
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report.write(args.report)
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if __name__ == "__main__":
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main()
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