prompt: We are currently solving the following issue within our repository. Here is the issue text:
  --- BEGIN ISSUE ---
  Lint warning on Nextflow minimum version badge
  ### Description of the bug
  
  `nf-core lint` complains that the minimum version badge for Nextflow could not found, however it was present in the `README.md`.
  It occurred after the `template-merge-2.4`
  It appears to be a bug.
  
  
  
  ### Command used and terminal output
  
  ```console
  (nextflow2) rnavar$ nf-core lint
  
  
  
                                            ,--./,-.
  
            ___     __   __   __   ___     /,-._.--~\
  
      |\ | |__  __ /  ` /  \ |__) |__         }  {
  
      | \| |       \__, \__/ |  \ |___     \`-._,-`-,
  
                                            `._,._,'
  
  
  
      nf-core/tools version 2.4.1 - https://nf-co.re
  
  
  
  
  
  INFO     Testing pipeline: .                                                                                                                                                                __init__.py:244
  
  
  
  ╭─ [!] 1 Pipeline Test Warning ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
  
  │                                                                                                                                                                                                         │
  
  │ readme: README did not have a Nextflow minimum version badge.                                                                                                                                           │
  
  │                                                                                                                                                                                                         │
  
  ╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
  ```
  
  
  ### System information
  
  _No response_
  
  --- 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 #!/usr/bin/env python
  2 
  3 import os
  4 import re
  5 
  6 
  7 def readme(self):
  8     """Repository ``README.md`` tests
  9 
  10     The ``README.md`` files for a project are very important and must meet some requirements:
  11 
  12     * Nextflow badge
  13 
  14       * If no Nextflow badge is found, a warning is given
  15       * If a badge is found but the version doesn't match the minimum version in the config file, the test fails
  16       * Example badge code:
  17 
  18         .. code-block:: md
  19 
  20            [![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A50.27.6-brightgreen.svg)](https://www.nextflow.io/)
  21 
  22     * Bioconda badge
  23 
  24       * If your pipeline contains a file called ``environment.yml`` in the root directory, a bioconda badge is required
  25       * Required badge code:
  26 
  27         .. code-block:: md
  28 
  29            [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](https://bioconda.github.io/)
  30 
  31     .. 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.
  32     """
  33     passed = []
  34     warned = []
  35     failed = []
  36 
  37     with open(os.path.join(self.wf_path, "README.md"), "r") as fh:
  38         content = fh.read()
  39 
  40     # Check that there is a readme badge showing the minimum required version of Nextflow
  41     # [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg?labelColor=000000)](https://www.nextflow.io/)
  42     # and that it has the correct version
  43     nf_badge_re = r"\[!\[Nextflow\]\(https://img\.shields\.io/badge/nextflow%20DSL2-%E2%89%A5([\d\.]+)-23aa62\.svg\?labelColor=000000\)\]\(https://www\.nextflow\.io/\)"
  44     match = re.search(nf_badge_re, content)
  45     if match:
  46         nf_badge_version = match.group(1).strip("'\"")
  47         try:
  48             assert nf_badge_version == self.minNextflowVersion
  49         except (AssertionError, KeyError):
  50             failed.append(
  51                 "README Nextflow minimum version badge does not match config. Badge: `{}`, Config: `{}`".format(
  52                     nf_badge_version, self.minNextflowVersion
  53                 )
  54             )
  55         else:
  56             passed.append(
  57                 "README Nextflow minimum version badge matched config. Badge: `{}`, Config: `{}`".format(
  58                     nf_badge_version, self.minNextflowVersion
  59                 )
  60             )
  61     else:
  62         warned.append("README did not have a Nextflow minimum version badge.")
  63 
  64     # Check that the minimum version mentioned in the quick start section is consistent
  65     # Looking for: "1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.10.3`)"
  66     nf_version_re = r"1\.\s*Install\s*\[`Nextflow`\]\(https://www.nextflow.io/docs/latest/getstarted.html#installation\)\s*\(`>=(\d*\.\d*\.\d*)`\)"
  67     match = re.search(nf_version_re, content)
  68     if match:
  69         nf_quickstart_version = match.group(1)
  70         try:
  71             assert nf_quickstart_version == self.minNextflowVersion
  72         except (AssertionError, KeyError):
  73             failed.append(
  74                 f"README Nextflow minimium version in Quick Start section does not match config. README: `{nf_quickstart_version}`, Config `{self.minNextflowVersion}`"
  75             )
  76         else:
  77             passed.append(
  78                 f"README Nextflow minimum version in Quick Start section matched config. README: `{nf_quickstart_version}`, Config: `{self.minNextflowVersion}`"
  79             )
  80     else:
  81         warned.append("README did not have a Nextflow minimum version mentioned in Quick Start section.")
  82 
  83     return {"passed": passed, "warned": warned, "failed": failed}
  84
  ```
  --- 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
  @@ -38,9 +38,9 @@
           content = fh.read()
   
       # 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?labelColor=000000)](https://www.nextflow.io/)
  +    # [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg)](https://www.nextflow.io/)
       # and that it has the correct version
  -    nf_badge_re = r"\[!\[Nextflow\]\(https://img\.shields\.io/badge/nextflow%20DSL2-%E2%89%A5([\d\.]+)-23aa62\.svg\?labelColor=000000\)\]\(https://www\.nextflow\.io/\)"
  +    nf_badge_re = r"\[!\[Nextflow\]\(https://img\.shields\.io/badge/nextflow%20DSL2-%E2%89%A5([\d\.]+)-23aa62\.svg\)\]\(https://www\.nextflow\.io/\)"
       match = re.search(nf_badge_re, content)
       if match:
           nf_badge_version = match.group(1).strip("'\"")
  
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@@ -38,9 +38,9 @@\n         content = fh.read()\n \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?labelColor=000000)](https://www.nextflow.io/)\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([\\d\\.]+)-23aa62\\.svg\\?labelColor=000000\\)\\]\\(https://www\\.nextflow\\.io/\\)\"\n+    nf_badge_re = r\"\\[!\\[Nextflow\\]\\(https://img\\.shields\\.io/badge/nextflow%20DSL2-%E2%89%A5([\\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", "issue": "Lint warning on Nextflow minimum version badge\n### Description of the bug\n\n`nf-core lint` complains that the minimum version badge for Nextflow could not found, however it was present in the `README.md`.\r\nIt occurred after the `template-merge-2.4`\r\nIt appears to be a bug.\r\n\r\n\n\n### Command used and terminal output\n\n```console\n(nextflow2) rnavar$ nf-core lint\r\n\r\n\r\n\r\n                                          ,--./,-.\r\n\r\n          ___     __   __   __   ___     /,-._.--~\\\r\n\r\n    |\\ | |__  __ /  ` /  \\ |__) |__         }  {\r\n\r\n    | \\| |       \\__, \\__/ |  \\ |___     \\`-._,-`-,\r\n\r\n                                          `._,._,'\r\n\r\n\r\n\r\n    nf-core/tools version 2.4.1 - https://nf-co.re\r\n\r\n\r\n\r\n\r\n\r\nINFO     Testing pipeline: .                                                                                                                                                                __init__.py:244\r\n\r\n\r\n\r\n\u256d\u2500 [!] 1 Pipeline Test Warning \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256e\r\n\r\n\u2502                                                                                                                                                                                                         \u2502\r\n\r\n\u2502 readme: README did not have a Nextflow minimum version badge.                                                                                                                                           \u2502\r\n\r\n\u2502                                                                                                                                                                                                         \u2502\r\n\r\n\u2570\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256f\n```\n\n\n### System information\n\n_No response_\n", "before_files": [{"content": "#!/usr/bin/env python\n\nimport 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    with open(os.path.join(self.wf_path, \"README.md\"), \"r\") as fh:\n        content = fh.read()\n\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?labelColor=000000)](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([\\d\\.]+)-23aa62\\.svg\\?labelColor=000000\\)\\]\\(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            assert nf_badge_version == self.minNextflowVersion\n        except (AssertionError, KeyError):\n            failed.append(\n                \"README Nextflow minimum version badge does not match config. Badge: `{}`, Config: `{}`\".format(\n                    nf_badge_version, self.minNextflowVersion\n                )\n            )\n        else:\n            passed.append(\n                \"README Nextflow minimum version badge matched config. Badge: `{}`, Config: `{}`\".format(\n                    nf_badge_version, self.minNextflowVersion\n                )\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            assert nf_quickstart_version == self.minNextflowVersion\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": "#!/usr/bin/env python\n\nimport 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    with open(os.path.join(self.wf_path, \"README.md\"), \"r\") as fh:\n        content = fh.read()\n\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([\\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            assert nf_badge_version == self.minNextflowVersion\n        except (AssertionError, KeyError):\n            failed.append(\n                \"README Nextflow minimum version badge does not match config. Badge: `{}`, Config: `{}`\".format(\n                    nf_badge_version, self.minNextflowVersion\n                )\n            )\n        else:\n            passed.append(\n                \"README Nextflow minimum version badge matched config. Badge: `{}`, Config: `{}`\".format(\n                    nf_badge_version, self.minNextflowVersion\n                )\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            assert nf_quickstart_version == self.minNextflowVersion\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"}]}