prompt: We are currently solving the following issue within our repository. Here is the issue text:
  --- BEGIN ISSUE ---
  Space missing in tip message for --fix files_unchanged
  <!--
  # nf-core/tools bug report
  
  Hi there!
  
  Thanks for telling us about a problem with the nf-core/tools package.
  Please delete this text and anything that's not relevant from the template below:
  -->
  
  ## Description of the bug
  
  a space is missing before `--fix files_unchanged`
  
  ```
  Tip: Some of these linting errors can automatically be resolved with the 
  following command:
  
      nf-core lint --dir /home/runner/work/rnavar/rnavar--fix files_unchanged
  ```
  
  ## Steps to reproduce
  
  https://github.com/nf-core/rnavar/runs/4317868056?check_suite_focus=true#step:6:100
  
  ## Expected behaviour
  
  <!-- A clear and concise description of what you expected to happen. -->
  
  ## System
  
  - Hardware: <!-- [e.g. HPC, Desktop, Cloud...] -->
  - Executor: <!-- [e.g. slurm, local, awsbatch...] -->
  - OS: <!-- [e.g. CentOS Linux, macOS, Linux Mint...] -->
  - Version of nf-core/tools: <!-- [e.g. 1.1, 1.5, 1.8.2...] -->
  - Python version: <!-- [e.g. 3.7, 3.8...] -->
  
  ## Nextflow Installation
  
  - Version: <!-- [e.g. 19.10.0] -->
  
  ## Additional context
  
  <!-- Add any other context about the problem here. -->
  
  
  --- END ISSUE ---
  
  Below are some code segments, each from a relevant file. One or more of these files may contain bugs.
  --- BEGIN FILES ---
  Path: `nf_core/lint_utils.py`
  Content:
  ```
  1 import rich
  2 from rich.console import Console
  3 from rich.table import Table
  4 import logging
  5 
  6 import nf_core.utils
  7 
  8 log = logging.getLogger(__name__)
  9 
  10 # Create a console used by all lint tests
  11 console = Console(force_terminal=nf_core.utils.rich_force_colors())
  12 
  13 
  14 def print_joint_summary(lint_obj, module_lint_obj):
  15     """Print a joint summary of the general pipe lint tests and the module lint tests"""
  16     nbr_passed = len(lint_obj.passed) + len(module_lint_obj.passed)
  17     nbr_ignored = len(lint_obj.ignored)
  18     nbr_fixed = len(lint_obj.fixed)
  19     nbr_warned = len(lint_obj.warned) + len(module_lint_obj.warned)
  20     nbr_failed = len(lint_obj.failed) + len(module_lint_obj.failed)
  21 
  22     def _s(some_length):
  23         return "" if some_length == 1 else "s"
  24 
  25     summary_colour = "red" if nbr_failed > 0 else "green"
  26     table = Table(box=rich.box.ROUNDED, style=summary_colour)
  27     table.add_column(f"LINT RESULTS SUMMARY".format(nbr_passed), no_wrap=True)
  28     table.add_row(r"[green][✔] {:>3} Test{} Passed".format(nbr_passed, _s(nbr_passed)))
  29     if nbr_fixed:
  30         table.add_row(r"[bright blue][?] {:>3} Test{} Fixed".format(nbr_fixed, _s(nbr_fixed)))
  31     table.add_row(r"[grey58][?] {:>3} Test{} Ignored".format(nbr_ignored, _s(nbr_ignored)))
  32     table.add_row(r"[yellow][!] {:>3} Test Warning{}".format(nbr_warned, _s(nbr_warned)))
  33     table.add_row(r"[red][✗] {:>3} Test{} Failed".format(nbr_failed, _s(nbr_failed)))
  34     console.print(table)
  35 
  36 
  37 def print_fixes(lint_obj, module_lint_obj):
  38     """Prints available and applied fixes"""
  39 
  40     if len(lint_obj.could_fix):
  41         fix_cmd = "nf-core lint {}--fix {}".format(
  42             "" if lint_obj.wf_path == "." else f"--dir {lint_obj.wf_path}", " --fix ".join(lint_obj.could_fix)
  43         )
  44         console.print(
  45             f"\nTip: Some of these linting errors can automatically be resolved with the following command:\n\n[blue]    {fix_cmd}\n"
  46         )
  47     if len(lint_obj.fix):
  48         console.print(
  49             "Automatic fixes applied. Please check with 'git diff' and revert any changes you do not want with 'git checkout <file>'."
  50         )
  51
  ```
  --- END FILES ---
  
  Please first localize the bug based on the issue statement, and then generate a patch according to the `git diff` format fenced by three backticks.
  
  Here is an example:
  
  ```diff
  diff --git a/examples/server_async.py b/examples/server_async.py
  --- a/examples/server_async.py
  +++ b/examples/server_async.py
  @@ -313,4 +313,4 @@
   
   
   if __name__ == "__main__":
  -    asyncio.run(run_async_server("."), debug=True)
  +    asyncio.run(run_async_server(), debug=True)
  diff --git a/examples/server_sync.py b/examples/server_sync.py
  --- a/examples/server_sync.py
  +++ b/examples/server_sync.py
  @@ -313,5 +313,5 @@
   
   
   if __name__ == "__main__":
  -    server = run_sync_server(".")
  +    server = run_sync_server()
       server.shutdown()
  
  ```
  
golden_diff: diff --git a/nf_core/lint_utils.py b/nf_core/lint_utils.py
  --- a/nf_core/lint_utils.py
  +++ b/nf_core/lint_utils.py
  @@ -38,7 +38,7 @@
       """Prints available and applied fixes"""
   
       if len(lint_obj.could_fix):
  -        fix_cmd = "nf-core lint {}--fix {}".format(
  +        fix_cmd = "nf-core lint {} --fix {}".format(
               "" if lint_obj.wf_path == "." else f"--dir {lint_obj.wf_path}", " --fix ".join(lint_obj.could_fix)
           )
           console.print(
  
verification_info: {"golden_diff": "diff --git a/nf_core/lint_utils.py b/nf_core/lint_utils.py\n--- a/nf_core/lint_utils.py\n+++ b/nf_core/lint_utils.py\n@@ -38,7 +38,7 @@\n     \"\"\"Prints available and applied fixes\"\"\"\n \n     if len(lint_obj.could_fix):\n-        fix_cmd = \"nf-core lint {}--fix {}\".format(\n+        fix_cmd = \"nf-core lint {} --fix {}\".format(\n             \"\" if lint_obj.wf_path == \".\" else f\"--dir {lint_obj.wf_path}\", \" --fix \".join(lint_obj.could_fix)\n         )\n         console.print(\n", "issue": "Space missing in tip message for --fix files_unchanged\n<!--\r\n# nf-core/tools bug report\r\n\r\nHi there!\r\n\r\nThanks for telling us about a problem with the nf-core/tools package.\r\nPlease delete this text and anything that's not relevant from the template below:\r\n-->\r\n\r\n## Description of the bug\r\n\r\na space is missing before `--fix files_unchanged`\r\n\r\n```\r\nTip: Some of these linting errors can automatically be resolved with the \r\nfollowing command:\r\n\r\n    nf-core lint --dir /home/runner/work/rnavar/rnavar--fix files_unchanged\r\n```\r\n\r\n## Steps to reproduce\r\n\r\nhttps://github.com/nf-core/rnavar/runs/4317868056?check_suite_focus=true#step:6:100\r\n\r\n## Expected behaviour\r\n\r\n<!-- A clear and concise description of what you expected to happen. -->\r\n\r\n## System\r\n\r\n- Hardware: <!-- [e.g. HPC, Desktop, Cloud...] -->\r\n- Executor: <!-- [e.g. slurm, local, awsbatch...] -->\r\n- OS: <!-- [e.g. CentOS Linux, macOS, Linux Mint...] -->\r\n- Version of nf-core/tools: <!-- [e.g. 1.1, 1.5, 1.8.2...] -->\r\n- Python version: <!-- [e.g. 3.7, 3.8...] -->\r\n\r\n## Nextflow Installation\r\n\r\n- Version: <!-- [e.g. 19.10.0] -->\r\n\r\n## Additional context\r\n\r\n<!-- Add any other context about the problem here. -->\r\n\n", "before_files": [{"content": "import rich\nfrom rich.console import Console\nfrom rich.table import Table\nimport logging\n\nimport nf_core.utils\n\nlog = logging.getLogger(__name__)\n\n# Create a console used by all lint tests\nconsole = Console(force_terminal=nf_core.utils.rich_force_colors())\n\n\ndef print_joint_summary(lint_obj, module_lint_obj):\n    \"\"\"Print a joint summary of the general pipe lint tests and the module lint tests\"\"\"\n    nbr_passed = len(lint_obj.passed) + len(module_lint_obj.passed)\n    nbr_ignored = len(lint_obj.ignored)\n    nbr_fixed = len(lint_obj.fixed)\n    nbr_warned = len(lint_obj.warned) + len(module_lint_obj.warned)\n    nbr_failed = len(lint_obj.failed) + len(module_lint_obj.failed)\n\n    def _s(some_length):\n        return \"\" if some_length == 1 else \"s\"\n\n    summary_colour = \"red\" if nbr_failed > 0 else \"green\"\n    table = Table(box=rich.box.ROUNDED, style=summary_colour)\n    table.add_column(f\"LINT RESULTS SUMMARY\".format(nbr_passed), no_wrap=True)\n    table.add_row(r\"[green][\u2714] {:>3} Test{} Passed\".format(nbr_passed, _s(nbr_passed)))\n    if nbr_fixed:\n        table.add_row(r\"[bright blue][?] {:>3} Test{} Fixed\".format(nbr_fixed, _s(nbr_fixed)))\n    table.add_row(r\"[grey58][?] {:>3} Test{} Ignored\".format(nbr_ignored, _s(nbr_ignored)))\n    table.add_row(r\"[yellow][!] {:>3} Test Warning{}\".format(nbr_warned, _s(nbr_warned)))\n    table.add_row(r\"[red][\u2717] {:>3} Test{} Failed\".format(nbr_failed, _s(nbr_failed)))\n    console.print(table)\n\n\ndef print_fixes(lint_obj, module_lint_obj):\n    \"\"\"Prints available and applied fixes\"\"\"\n\n    if len(lint_obj.could_fix):\n        fix_cmd = \"nf-core lint {}--fix {}\".format(\n            \"\" if lint_obj.wf_path == \".\" else f\"--dir {lint_obj.wf_path}\", \" --fix \".join(lint_obj.could_fix)\n        )\n        console.print(\n            f\"\\nTip: Some of these linting errors can automatically be resolved with the following command:\\n\\n[blue]    {fix_cmd}\\n\"\n        )\n    if len(lint_obj.fix):\n        console.print(\n            \"Automatic fixes applied. Please check with 'git diff' and revert any changes you do not want with 'git checkout <file>'.\"\n        )\n", "path": "nf_core/lint_utils.py"}], "after_files": [{"content": "import rich\nfrom rich.console import Console\nfrom rich.table import Table\nimport logging\n\nimport nf_core.utils\n\nlog = logging.getLogger(__name__)\n\n# Create a console used by all lint tests\nconsole = Console(force_terminal=nf_core.utils.rich_force_colors())\n\n\ndef print_joint_summary(lint_obj, module_lint_obj):\n    \"\"\"Print a joint summary of the general pipe lint tests and the module lint tests\"\"\"\n    nbr_passed = len(lint_obj.passed) + len(module_lint_obj.passed)\n    nbr_ignored = len(lint_obj.ignored)\n    nbr_fixed = len(lint_obj.fixed)\n    nbr_warned = len(lint_obj.warned) + len(module_lint_obj.warned)\n    nbr_failed = len(lint_obj.failed) + len(module_lint_obj.failed)\n\n    def _s(some_length):\n        return \"\" if some_length == 1 else \"s\"\n\n    summary_colour = \"red\" if nbr_failed > 0 else \"green\"\n    table = Table(box=rich.box.ROUNDED, style=summary_colour)\n    table.add_column(f\"LINT RESULTS SUMMARY\".format(nbr_passed), no_wrap=True)\n    table.add_row(r\"[green][\u2714] {:>3} Test{} Passed\".format(nbr_passed, _s(nbr_passed)))\n    if nbr_fixed:\n        table.add_row(r\"[bright blue][?] {:>3} Test{} Fixed\".format(nbr_fixed, _s(nbr_fixed)))\n    table.add_row(r\"[grey58][?] {:>3} Test{} Ignored\".format(nbr_ignored, _s(nbr_ignored)))\n    table.add_row(r\"[yellow][!] {:>3} Test Warning{}\".format(nbr_warned, _s(nbr_warned)))\n    table.add_row(r\"[red][\u2717] {:>3} Test{} Failed\".format(nbr_failed, _s(nbr_failed)))\n    console.print(table)\n\n\ndef print_fixes(lint_obj, module_lint_obj):\n    \"\"\"Prints available and applied fixes\"\"\"\n\n    if len(lint_obj.could_fix):\n        fix_cmd = \"nf-core lint {} --fix {}\".format(\n            \"\" if lint_obj.wf_path == \".\" else f\"--dir {lint_obj.wf_path}\", \" --fix \".join(lint_obj.could_fix)\n        )\n        console.print(\n            f\"\\nTip: Some of these linting errors can automatically be resolved with the following command:\\n\\n[blue]    {fix_cmd}\\n\"\n        )\n    if len(lint_obj.fix):\n        console.print(\n            \"Automatic fixes applied. Please check with 'git diff' and revert any changes you do not want with 'git checkout <file>'.\"\n        )\n", "path": "nf_core/lint_utils.py"}]}