prompt: We are currently solving the following issue within our repository. Here is the issue text:
  --- BEGIN ISSUE ---
  Bump minimum required Nextflow version
  ### Description of feature
  
  Latest stable release brings lots of new features that we probably want to use at module level (eg. `bin` directories).
  
  --- 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/readme.py`
  Content:
  ```
  1 import os
  2 import re
  3 
  4 
  5 def readme(self):
  6     """Repository ``README.md`` tests
  7 
  8     The ``README.md`` files for a project are very important and must meet some requirements:
  9 
  10     * Nextflow badge
  11 
  12       * If no Nextflow badge is found, a warning is given
  13       * If a badge is found but the version doesn't match the minimum version in the config file, the test fails
  14       * Example badge code:
  15 
  16         .. code-block:: md
  17 
  18            [![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A50.27.6-brightgreen.svg)](https://www.nextflow.io/)
  19 
  20     * Bioconda badge
  21 
  22       * If your pipeline contains a file called ``environment.yml`` in the root directory, a bioconda badge is required
  23       * Required badge code:
  24 
  25         .. code-block:: md
  26 
  27            [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](https://bioconda.github.io/)
  28 
  29     .. note:: These badges are a markdown image ``![alt-text](<image URL>)`` *inside* a markdown link ``[markdown image](<link URL>)``, so a bit fiddly to write.
  30     """
  31     passed = []
  32     warned = []
  33     failed = []
  34 
  35     # Remove field that should be ignored according to the linting config
  36     ignore_configs = self.lint_config.get("readme", [])
  37 
  38     with open(os.path.join(self.wf_path, "README.md"), "r") as fh:
  39         content = fh.read()
  40 
  41     if "nextflow_badge" not in ignore_configs:
  42         # Check that there is a readme badge showing the minimum required version of Nextflow
  43         # [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg)](https://www.nextflow.io/)
  44         # and that it has the correct version
  45         nf_badge_re = r"\[!\[Nextflow\]\(https://img\.shields\.io/badge/nextflow%20DSL2-!?(?:%E2%89%A5|%3E%3D)([\d\.]+)-23aa62\.svg\)\]\(https://www\.nextflow\.io/\)"
  46         match = re.search(nf_badge_re, content)
  47         if match:
  48             nf_badge_version = match.group(1).strip("'\"")
  49             try:
  50                 if nf_badge_version != self.minNextflowVersion:
  51                     raise AssertionError()
  52             except (AssertionError, KeyError):
  53                 failed.append(
  54                     f"README Nextflow minimum version badge does not match config. Badge: `{nf_badge_version}`, "
  55                     f"Config: `{self.minNextflowVersion}`"
  56                 )
  57             else:
  58                 passed.append(
  59                     f"README Nextflow minimum version badge matched config. Badge: `{nf_badge_version}`, "
  60                     f"Config: `{self.minNextflowVersion}`"
  61                 )
  62         else:
  63             warned.append("README did not have a Nextflow minimum version badge.")
  64 
  65     # Check that the minimum version mentioned in the quick start section is consistent
  66     # Looking for: "1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.10.3`)"
  67     nf_version_re = r"1\.\s*Install\s*\[`Nextflow`\]\(https://www.nextflow.io/docs/latest/getstarted.html#installation\)\s*\(`>=(\d*\.\d*\.\d*)`\)"
  68     match = re.search(nf_version_re, content)
  69     if match:
  70         nf_quickstart_version = match.group(1)
  71         try:
  72             if nf_quickstart_version != self.minNextflowVersion:
  73                 raise AssertionError()
  74         except (AssertionError, KeyError):
  75             failed.append(
  76                 f"README Nextflow minimium version in Quick Start section does not match config. README: `{nf_quickstart_version}`, Config `{self.minNextflowVersion}`"
  77             )
  78         else:
  79             passed.append(
  80                 f"README Nextflow minimum version in Quick Start section matched config. README: `{nf_quickstart_version}`, Config: `{self.minNextflowVersion}`"
  81             )
  82     else:
  83         warned.append("README did not have a Nextflow minimum version mentioned in Quick Start section.")
  84 
  85     return {"passed": passed, "warned": warned, "failed": failed}
  86
  ```
  --- 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/readme.py b/nf_core/lint/readme.py
  --- a/nf_core/lint/readme.py
  +++ b/nf_core/lint/readme.py
  @@ -40,7 +40,7 @@
   
       if "nextflow_badge" not in ignore_configs:
           # Check that there is a readme badge showing the minimum required version of Nextflow
  -        # [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg)](https://www.nextflow.io/)
  +        # [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/)
           # and that it has the correct version
           nf_badge_re = r"\[!\[Nextflow\]\(https://img\.shields\.io/badge/nextflow%20DSL2-!?(?:%E2%89%A5|%3E%3D)([\d\.]+)-23aa62\.svg\)\]\(https://www\.nextflow\.io/\)"
           match = re.search(nf_badge_re, content)
  @@ -63,7 +63,7 @@
               warned.append("README did not have a Nextflow minimum version badge.")
   
       # Check that the minimum version mentioned in the quick start section is consistent
  -    # Looking for: "1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.10.3`)"
  +    # Looking for: "1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=22.10.1`)"
       nf_version_re = r"1\.\s*Install\s*\[`Nextflow`\]\(https://www.nextflow.io/docs/latest/getstarted.html#installation\)\s*\(`>=(\d*\.\d*\.\d*)`\)"
       match = re.search(nf_version_re, content)
       if match:
  
verification_info: {"golden_diff": "diff --git a/nf_core/lint/readme.py b/nf_core/lint/readme.py\n--- a/nf_core/lint/readme.py\n+++ b/nf_core/lint/readme.py\n@@ -40,7 +40,7 @@\n \n     if \"nextflow_badge\" not in ignore_configs:\n         # Check that there is a readme badge showing the minimum required version of Nextflow\n-        # [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg)](https://www.nextflow.io/)\n+        # [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/)\n         # and that it has the correct version\n         nf_badge_re = r\"\\[!\\[Nextflow\\]\\(https://img\\.shields\\.io/badge/nextflow%20DSL2-!?(?:%E2%89%A5|%3E%3D)([\\d\\.]+)-23aa62\\.svg\\)\\]\\(https://www\\.nextflow\\.io/\\)\"\n         match = re.search(nf_badge_re, content)\n@@ -63,7 +63,7 @@\n             warned.append(\"README did not have a Nextflow minimum version badge.\")\n \n     # Check that the minimum version mentioned in the quick start section is consistent\n-    # Looking for: \"1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.10.3`)\"\n+    # Looking for: \"1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=22.10.1`)\"\n     nf_version_re = r\"1\\.\\s*Install\\s*\\[`Nextflow`\\]\\(https://www.nextflow.io/docs/latest/getstarted.html#installation\\)\\s*\\(`>=(\\d*\\.\\d*\\.\\d*)`\\)\"\n     match = re.search(nf_version_re, content)\n     if match:\n", "issue": "Bump minimum required Nextflow version\n### Description of feature\n\nLatest stable release brings lots of new features that we probably want to use at module level (eg. `bin` directories).\n", "before_files": [{"content": "import os\nimport re\n\n\ndef readme(self):\n    \"\"\"Repository ``README.md`` tests\n\n    The ``README.md`` files for a project are very important and must meet some requirements:\n\n    * Nextflow badge\n\n      * If no Nextflow badge is found, a warning is given\n      * If a badge is found but the version doesn't match the minimum version in the config file, the test fails\n      * Example badge code:\n\n        .. code-block:: md\n\n           [![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A50.27.6-brightgreen.svg)](https://www.nextflow.io/)\n\n    * Bioconda badge\n\n      * If your pipeline contains a file called ``environment.yml`` in the root directory, a bioconda badge is required\n      * Required badge code:\n\n        .. code-block:: md\n\n           [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](https://bioconda.github.io/)\n\n    .. note:: These badges are a markdown image ``![alt-text](<image URL>)`` *inside* a markdown link ``[markdown image](<link URL>)``, so a bit fiddly to write.\n    \"\"\"\n    passed = []\n    warned = []\n    failed = []\n\n    # Remove field that should be ignored according to the linting config\n    ignore_configs = self.lint_config.get(\"readme\", [])\n\n    with open(os.path.join(self.wf_path, \"README.md\"), \"r\") as fh:\n        content = fh.read()\n\n    if \"nextflow_badge\" not in ignore_configs:\n        # Check that there is a readme badge showing the minimum required version of Nextflow\n        # [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg)](https://www.nextflow.io/)\n        # and that it has the correct version\n        nf_badge_re = r\"\\[!\\[Nextflow\\]\\(https://img\\.shields\\.io/badge/nextflow%20DSL2-!?(?:%E2%89%A5|%3E%3D)([\\d\\.]+)-23aa62\\.svg\\)\\]\\(https://www\\.nextflow\\.io/\\)\"\n        match = re.search(nf_badge_re, content)\n        if match:\n            nf_badge_version = match.group(1).strip(\"'\\\"\")\n            try:\n                if nf_badge_version != self.minNextflowVersion:\n                    raise AssertionError()\n            except (AssertionError, KeyError):\n                failed.append(\n                    f\"README Nextflow minimum version badge does not match config. Badge: `{nf_badge_version}`, \"\n                    f\"Config: `{self.minNextflowVersion}`\"\n                )\n            else:\n                passed.append(\n                    f\"README Nextflow minimum version badge matched config. Badge: `{nf_badge_version}`, \"\n                    f\"Config: `{self.minNextflowVersion}`\"\n                )\n        else:\n            warned.append(\"README did not have a Nextflow minimum version badge.\")\n\n    # Check that the minimum version mentioned in the quick start section is consistent\n    # Looking for: \"1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.10.3`)\"\n    nf_version_re = r\"1\\.\\s*Install\\s*\\[`Nextflow`\\]\\(https://www.nextflow.io/docs/latest/getstarted.html#installation\\)\\s*\\(`>=(\\d*\\.\\d*\\.\\d*)`\\)\"\n    match = re.search(nf_version_re, content)\n    if match:\n        nf_quickstart_version = match.group(1)\n        try:\n            if nf_quickstart_version != self.minNextflowVersion:\n                raise AssertionError()\n        except (AssertionError, KeyError):\n            failed.append(\n                f\"README Nextflow minimium version in Quick Start section does not match config. README: `{nf_quickstart_version}`, Config `{self.minNextflowVersion}`\"\n            )\n        else:\n            passed.append(\n                f\"README Nextflow minimum version in Quick Start section matched config. README: `{nf_quickstart_version}`, Config: `{self.minNextflowVersion}`\"\n            )\n    else:\n        warned.append(\"README did not have a Nextflow minimum version mentioned in Quick Start section.\")\n\n    return {\"passed\": passed, \"warned\": warned, \"failed\": failed}\n", "path": "nf_core/lint/readme.py"}], "after_files": [{"content": "import os\nimport re\n\n\ndef readme(self):\n    \"\"\"Repository ``README.md`` tests\n\n    The ``README.md`` files for a project are very important and must meet some requirements:\n\n    * Nextflow badge\n\n      * If no Nextflow badge is found, a warning is given\n      * If a badge is found but the version doesn't match the minimum version in the config file, the test fails\n      * Example badge code:\n\n        .. code-block:: md\n\n           [![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A50.27.6-brightgreen.svg)](https://www.nextflow.io/)\n\n    * Bioconda badge\n\n      * If your pipeline contains a file called ``environment.yml`` in the root directory, a bioconda badge is required\n      * Required badge code:\n\n        .. code-block:: md\n\n           [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](https://bioconda.github.io/)\n\n    .. note:: These badges are a markdown image ``![alt-text](<image URL>)`` *inside* a markdown link ``[markdown image](<link URL>)``, so a bit fiddly to write.\n    \"\"\"\n    passed = []\n    warned = []\n    failed = []\n\n    # Remove field that should be ignored according to the linting config\n    ignore_configs = self.lint_config.get(\"readme\", [])\n\n    with open(os.path.join(self.wf_path, \"README.md\"), \"r\") as fh:\n        content = fh.read()\n\n    if \"nextflow_badge\" not in ignore_configs:\n        # Check that there is a readme badge showing the minimum required version of Nextflow\n        # [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/)\n        # and that it has the correct version\n        nf_badge_re = r\"\\[!\\[Nextflow\\]\\(https://img\\.shields\\.io/badge/nextflow%20DSL2-!?(?:%E2%89%A5|%3E%3D)([\\d\\.]+)-23aa62\\.svg\\)\\]\\(https://www\\.nextflow\\.io/\\)\"\n        match = re.search(nf_badge_re, content)\n        if match:\n            nf_badge_version = match.group(1).strip(\"'\\\"\")\n            try:\n                if nf_badge_version != self.minNextflowVersion:\n                    raise AssertionError()\n            except (AssertionError, KeyError):\n                failed.append(\n                    f\"README Nextflow minimum version badge does not match config. Badge: `{nf_badge_version}`, \"\n                    f\"Config: `{self.minNextflowVersion}`\"\n                )\n            else:\n                passed.append(\n                    f\"README Nextflow minimum version badge matched config. Badge: `{nf_badge_version}`, \"\n                    f\"Config: `{self.minNextflowVersion}`\"\n                )\n        else:\n            warned.append(\"README did not have a Nextflow minimum version badge.\")\n\n    # Check that the minimum version mentioned in the quick start section is consistent\n    # Looking for: \"1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=22.10.1`)\"\n    nf_version_re = r\"1\\.\\s*Install\\s*\\[`Nextflow`\\]\\(https://www.nextflow.io/docs/latest/getstarted.html#installation\\)\\s*\\(`>=(\\d*\\.\\d*\\.\\d*)`\\)\"\n    match = re.search(nf_version_re, content)\n    if match:\n        nf_quickstart_version = match.group(1)\n        try:\n            if nf_quickstart_version != self.minNextflowVersion:\n                raise AssertionError()\n        except (AssertionError, KeyError):\n            failed.append(\n                f\"README Nextflow minimium version in Quick Start section does not match config. README: `{nf_quickstart_version}`, Config `{self.minNextflowVersion}`\"\n            )\n        else:\n            passed.append(\n                f\"README Nextflow minimum version in Quick Start section matched config. README: `{nf_quickstart_version}`, Config: `{self.minNextflowVersion}`\"\n            )\n    else:\n        warned.append(\"README did not have a Nextflow minimum version mentioned in Quick Start section.\")\n\n    return {\"passed\": passed, \"warned\": warned, \"failed\": failed}\n", "path": "nf_core/lint/readme.py"}]}