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| # nf-core/nanoseq bug report | ||
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| Hi there! | ||
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| Thanks for telling us about a problem with the pipeline. Please delete this text and anything that's not relevant from the template below: | ||
| Thanks for telling us about a problem with the pipeline. | ||
| Please delete this text and anything that's not relevant from the template below: | ||
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| ## Describe the bug | ||
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| #### Describe the bug | ||
| A clear and concise description of what the bug is. | ||
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| #### Steps to reproduce | ||
| ## Steps to reproduce | ||
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| Steps to reproduce the behaviour: | ||
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| 1. Command line: `nextflow run ...` | ||
| 2. See error: _Please provide your error message_ | ||
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| #### Expected behaviour | ||
| ## Expected behaviour | ||
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| A clear and concise description of what you expected to happen. | ||
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| #### System: | ||
| - Hardware: [e.g. HPC, Desktop, Cloud...] | ||
| - Executor: [e.g. slurm, local, awsbatch...] | ||
| - OS: [e.g. CentOS Linux, macOS, Linux Mint...] | ||
| - Version [e.g. 7, 10.13.6, 18.3...] | ||
| ## System | ||
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| - Hardware: <!-- [e.g. HPC, Desktop, Cloud...] --> | ||
| - Executor: <!-- [e.g. slurm, local, awsbatch...] --> | ||
| - OS: <!-- [e.g. CentOS Linux, macOS, Linux Mint...] --> | ||
| - Version <!-- [e.g. 7, 10.13.6, 18.3...] --> | ||
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| ## Nextflow Installation | ||
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| - Version: <!-- [e.g. 19.10.0] --> | ||
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| ## Container engine | ||
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| #### Nextflow Installation: | ||
| - Version: [e.g. 0.31.0] | ||
| - Engine: <!-- [e.g. Conda, Docker or Singularity] --> | ||
| - version: <!-- [e.g. 1.0.0] --> | ||
| - Image tag: <!-- [e.g. nfcore/nanoseq:1.0.0] --> | ||
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| #### Container engine: | ||
| - Engine: [e.g. Conda, Docker or Singularity] | ||
| - version: [e.g. 1.0.0] | ||
| - Image tag: [e.g. nfcore/nanoseq:1.0.0] | ||
| ## Additional context | ||
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| #### Additional context | ||
| Add any other context about the problem here. |
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| # nf-core/nanoseq: Changelog | ||
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| The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) | ||
| and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html). | ||
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| ## v1.0dev - [date] | ||
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| Initial release of nf-core/nanoseq, created with the [nf-core](http://nf-co.re/) template. | ||
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| ### `Added` | ||
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| ### `Fixed` | ||
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| ### `Dependencies` | ||
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| ### `Deprecated` |
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| #!/usr/bin/env python | ||
| from __future__ import print_function | ||
| import argparse | ||
| import markdown | ||
| import os | ||
| import sys | ||
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| def convert_markdown(in_fn): | ||
| input_md = open(in_fn, mode="r", encoding="utf-8").read() | ||
| html = markdown.markdown( | ||
| "[TOC]\n" + input_md, | ||
| extensions = [ | ||
| 'pymdownx.extra', | ||
| 'pymdownx.b64', | ||
| 'pymdownx.highlight', | ||
| 'pymdownx.emoji', | ||
| 'pymdownx.tilde', | ||
| 'toc' | ||
| ], | ||
| extension_configs = { | ||
| 'pymdownx.b64': { | ||
| 'base_path': os.path.dirname(in_fn) | ||
| }, | ||
| 'pymdownx.highlight': { | ||
| 'noclasses': True | ||
| }, | ||
| 'toc': { | ||
| 'title': 'Table of Contents' | ||
| } | ||
| } | ||
| ) | ||
| return html | ||
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| def wrap_html(contents): | ||
| header = """<!DOCTYPE html><html> | ||
| <head> | ||
| <link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css" integrity="sha384-ggOyR0iXCbMQv3Xipma34MD+dH/1fQ784/j6cY/iJTQUOhcWr7x9JvoRxT2MZw1T" crossorigin="anonymous"> | ||
| <style> | ||
| body { | ||
| font-family: -apple-system,BlinkMacSystemFont,"Segoe UI",Roboto,"Helvetica Neue",Arial,"Noto Sans",sans-serif,"Apple Color Emoji","Segoe UI Emoji","Segoe UI Symbol","Noto Color Emoji"; | ||
| padding: 3em; | ||
| margin-right: 350px; | ||
| max-width: 100%; | ||
| } | ||
| .toc { | ||
| position: fixed; | ||
| right: 20px; | ||
| width: 300px; | ||
| padding-top: 20px; | ||
| overflow: scroll; | ||
| height: calc(100% - 3em - 20px); | ||
| } | ||
| .toctitle { | ||
| font-size: 1.8em; | ||
| font-weight: bold; | ||
| } | ||
| .toc > ul { | ||
| padding: 0; | ||
| margin: 1rem 0; | ||
| list-style-type: none; | ||
| } | ||
| .toc > ul ul { padding-left: 20px; } | ||
| .toc > ul > li > a { display: none; } | ||
| img { max-width: 800px; } | ||
| pre { | ||
| padding: 0.6em 1em; | ||
| } | ||
| h2 { | ||
| } | ||
| </style> | ||
| </head> | ||
| <body> | ||
| <div class="container"> | ||
| """ | ||
| footer = """ | ||
| </div> | ||
| </body> | ||
| </html> | ||
| """ | ||
| return header + contents + footer | ||
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| def parse_args(args=None): | ||
| parser = argparse.ArgumentParser() | ||
| parser.add_argument('mdfile', type=argparse.FileType('r'), nargs='?', | ||
| help='File to convert. Defaults to stdin.') | ||
| parser.add_argument('-o', '--out', type=argparse.FileType('w'), | ||
| default=sys.stdout, | ||
| help='Output file name. Defaults to stdout.') | ||
| return parser.parse_args(args) | ||
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| def main(args=None): | ||
| args = parse_args(args) | ||
| converted_md = convert_markdown(args.mdfile.name) | ||
| html = wrap_html(converted_md) | ||
| args.out.write(html) | ||
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| if __name__ == '__main__': | ||
| sys.exit(main()) |
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