pranathivemuri
commented
3 years ago @ewels Hi! Could you please give us a hint on why this lint error is occurring. Really appreciate your reply!
INFO Writing lint results to lint_results.md lint.py:72
╭───────────────────── Traceback (most recent call last) ──────────────────────╮
│ /opt/hostedtoolcache/Python/3.6.12/x64/bin/nf-core:8 in <module> │
│ ClassNotFound: no lexer for filename 'nf-core' found │
│ │
│ /opt/hostedtoolcache/Python/3.6.12/x64/lib/python3.6/site-packages/nf_core/_ │
│ _main__.py:56 in run_nf_core │
│ │
│ 53 │ stderr.print("\n\n") │
│ 54 │ │
│ 55 │ # Lanch the click cli │
│ ❱ 56 │ nf_core_cli() │
│ 57 │
│ 58 │
│ 59 # Customise the order of subcommands for --help │
│ │
│ /opt/hostedtoolcache/Python/3.6.12/x64/lib/python3.6/site-packages/click/cor │
│ e.py:829 in __call__ │
│ │
│ 826 │ │
│ 827 │ def __call__(self, *args, **kwargs): │
│ 828 │ │ """Alias for :meth:`main`.""" │
│ ❱ 829 │ │ return self.main(*args, **kwargs) │
│ 830 │
│ 831 │
│ 832 class Command(BaseCommand): │
│ │
│ /opt/hostedtoolcache/Python/3.6.12/x64/lib/python3.6/site-packages/click/cor │
│ e.py:782 in main │
│ │
│ 779 │ │ try: │
│ 780 │ │ │ try: │
│ 781 │ │ │ │ with self.make_context(prog_name, args, **extra) as c │
│ ❱ 782 │ │ │ │ │ rv = self.invoke(ctx) │
│ 783 │ │ │ │ │ if not standalone_mode: │
│ 784 │ │ │ │ │ │ return rv │
│ 785 │ │ │ │ │ # it's not safe to `ctx.exit(rv)` here! │
│ │
│ /opt/hostedtoolcache/Python/3.6.12/x64/lib/python3.6/site-packages/click/cor │
│ e.py:1259 in invoke │
│ │
│ 1256 │ │ │ │ Command.invoke(self, ctx) │
│ 1257 │ │ │ │ sub_ctx = cmd.make_context(cmd_name, args, parent=ctx │
│ 1258 │ │ │ │ with sub_ctx: │
│ ❱ 1259 │ │ │ │ │ return _process_result(sub_ctx.command.invoke(sub │
│ 1260 │ │ │
│ 1261 │ │ # In chain mode we create the contexts step by step, but afte │
│ 1262 │ │ # base command has been invoked. Because at that point we do │
│ │
│ /opt/hostedtoolcache/Python/3.6.12/x64/lib/python3.6/site-packages/click/cor │
│ e.py:1066 in invoke │
│ │
│ 1063 │ │ """ │
│ 1064 │ │ _maybe_show_deprecated_notice(self) │
│ 1065 │ │ if self.callback is not None: │
│ ❱ 1066 │ │ │ return ctx.invoke(self.callback, **ctx.params) │
│ 1067 │
│ 1068 │
│ 1069 class MultiCommand(Command): │
│ │
│ /opt/hostedtoolcache/Python/3.6.12/x64/lib/python3.6/site-packages/click/cor │
│ e.py:610 in invoke │
│ │
│ 607 │ │ args = args[2:] │
│ 608 │ │ with augment_usage_errors(self): │
│ 609 │ │ │ with ctx: │
│ ❱ 610 │ │ │ │ return callback(*args, **kwargs) │
│ 611 │ │
│ 612 │ def forward(*args, **kwargs): # noqa: B902 │
│ 613 │ │ """Similar to :meth:`invoke` but fills in default keyword │
│ │
│ /opt/hostedtoolcache/Python/3.6.12/x64/lib/python3.6/site-packages/nf_core/_ │
│ _main__.py:306 in lint │
│ │
│ 303 │ """ │
│ 304 │ │
│ 305 │ # Run the lint tests! │
│ ❱ 306 │ lint_obj = nf_core.lint.run_linting(pipeline_dir, release, show_pa │
│ json) │
│ 307 │ if len(lint_obj.failed) > 0: │
│ 308 │ │ sys.exit(1) │
│ 309 │
│ │
│ /opt/hostedtoolcache/Python/3.6.12/x64/lib/python3.6/site-packages/nf_core/l │
│ int.py:73 in run_linting │
│ │
│ 70 │ # Save results to Markdown file │
│ 71 │ if md_fn is not None: │
│ 72 │ │ log.info("Writing lint results to {}".format(md_fn)) │
│ ❱ 73 │ │ markdown = lint_obj.get_results_md() │
│ 74 │ │ with open(md_fn, "w") as fh: │
│ 75 │ │ │ fh.write(markdown) │
│ 76 │ │
│ │
│ /opt/hostedtoolcache/Python/3.6.12/x64/lib/python3.6/site-packages/nf_core/l │
│ int.py:1409 in get_results_md │
│ │
│ 1406 │ │ │ │ "\n".join( │
│ 1407 │ │ │ │ │ [ │
│ 1408 │ │ │ │ │ │ "* [Test #{0}](https://nf-co.re/errors#{0}) - │
│ self._strip_ansi_codes(msg, "`")) │
│ ❱ 1409 │ │ │ │ │ │ for eid, msg in self.warned │
│ 1410 │ │ │ │ │ ] │
│ 1411 │ │ │ │ ) │
│ 1412 │ │ │ ) │
│ │
│ /opt/hostedtoolcache/Python/3.6.12/x64/lib/python3.6/site-packages/nf_core/l │
│ int.py:1409 in <listcomp> │
│ │
│ 1406 │ │ │ │ "\n".join( │
│ 1407 │ │ │ │ │ [ │
│ 1408 │ │ │ │ │ │ "* [Test #{0}](https://nf-co.re/errors#{0}) - │
│ self._strip_ansi_codes(msg, "`")) │
│ ❱ 1409 │ │ │ │ │ │ for eid, msg in self.warned │
│ 1410 │ │ │ │ │ ] │
│ 1411 │ │ │ │ ) │
│ 1412 │ │ │ ) │
│ │
│ /opt/hostedtoolcache/Python/3.6.12/x64/lib/python3.6/site-packages/nf_core/l │
│ int.py:1495 in _strip_ansi_codes │
│ │
│ 1492 │ def _strip_ansi_codes(self, string, replace_with=""): │
│ 1493 │ │ # https://stackoverflow.com/a/14693789/713980 │
│ 1494 │ │ ansi_escape = re.compile(r"\x1B(?:[@-Z\\-_]|\[[0-?]*[ -/]*[@- │
│ ❱ 1495 │ │ return ansi_escape.sub(replace_with, string) │
╰──────────────────────────────────────────────────────────────────────────────╯
TypeError: expected string or bytes-like object
Error: Process completed with exit code 1.
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