From cb0d2903f51aa20f6c7aa4db90f3de4ebd07b003 Mon Sep 17 00:00:00 2001
From: Erik Danielsson <danielsson.erik.0@gmail.com>
Date: Wed, 4 Aug 2021 15:48:05 +0200
Subject: [PATCH 01/12] Update lint docs creation script to include modules

---
 docs/api/make_lint_md.py  | 54 +++++++++++++++++++++++++++++++++++++++
 docs/api/make_lint_rst.py | 34 ------------------------
 2 files changed, 54 insertions(+), 34 deletions(-)
 create mode 100644 docs/api/make_lint_md.py
 delete mode 100644 docs/api/make_lint_rst.py

diff --git a/docs/api/make_lint_md.py b/docs/api/make_lint_md.py
new file mode 100644
index 0000000000..6b54dc8682
--- /dev/null
+++ b/docs/api/make_lint_md.py
@@ -0,0 +1,54 @@
+#!/usr/bin/env python
+
+import fnmatch
+import os
+import nf_core.lint
+import nf_core.modules.lint
+
+
+def make_docs(docs_basedir, lint_tests, md_template):
+    # Get list of existing .md files
+    existing_docs = []
+    for fn in os.listdir(docs_basedir):
+        if fnmatch.fnmatch(fn, "*.md") and not fnmatch.fnmatch(fn, "index.md"):
+            existing_docs.append(os.path.join(docs_basedir, fn))
+
+    for test_name in lint_tests:
+        fn = os.path.join(docs_basedir, "{}.md".format(test_name))
+        if os.path.exists(fn):
+            existing_docs.remove(fn)
+        else:
+            with open(fn, "w") as fh:
+                fh.write(md_template.format(test_name))
+
+    for fn in existing_docs:
+        os.remove(fn)
+
+
+# Create the pipeline docs
+pipeline_docs_basedir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "_src", "pipeline_lint_tests")
+make_docs(
+    pipeline_docs_basedir,
+    nf_core.lint.PipelineLint._get_all_lint_tests(),
+    """# {0}
+
+    ```{eval-rst}
+    .. automethod:: nf_core.lint.PipelineLint.{0}
+    ```
+
+    """,
+)
+
+# Create the modules lint docs
+modules_docs_basedir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "_src", "modules_lint_tests")
+make_docs(
+    modules_docs_basedir,
+    nf_core.modules.lint.ModuleLint._get_all_lint_tests(),
+    """# {0}
+
+    ```{eval-rst}
+    .. automethod:: nf_core.modules.lint.ModuleLint.{0}
+    ```
+
+    """,
+)
diff --git a/docs/api/make_lint_rst.py b/docs/api/make_lint_rst.py
deleted file mode 100644
index 2e80e384ac..0000000000
--- a/docs/api/make_lint_rst.py
+++ /dev/null
@@ -1,34 +0,0 @@
-#!/usr/bin/env python
-
-import fnmatch
-import os
-import nf_core.lint
-
-docs_basedir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "_src", "pipeline_lint_tests")
-
-# Get list of existing .md files
-existing_docs = []
-for fn in os.listdir(docs_basedir):
-    if fnmatch.fnmatch(fn, "*.md") and not fnmatch.fnmatch(fn, "index.md"):
-        existing_docs.append(os.path.join(docs_basedir, fn))
-
-# Make .md file for each test name
-lint_obj = nf_core.lint.PipelineLint("", True)
-md_template = """# {0}
-
-```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.{0}
-```
-
-"""
-
-for test_name in lint_obj.lint_tests:
-    fn = os.path.join(docs_basedir, "{}.md".format(test_name))
-    if os.path.exists(fn):
-        existing_docs.remove(fn)
-    else:
-        with open(fn, "w") as fh:
-            fh.write(md_template.format(test_name))
-
-for fn in existing_docs:
-    os.remove(fn)

From 8805422edb65d1b31d6ae40fb38de2abdff6bc37 Mon Sep 17 00:00:00 2001
From: Erik Danielsson <danielsson.erik.0@gmail.com>
Date: Wed, 4 Aug 2021 17:34:26 +0200
Subject: [PATCH 02/12] Flesh out module lint tests descriptions, and create
 .md files

---
 .../_src/module_lint_tests/functions_nf.md    |  5 ++++
 docs/api/_src/module_lint_tests/index.md      |  9 +++++++
 docs/api/_src/module_lint_tests/main_nf.md    |  6 +++++
 docs/api/_src/module_lint_tests/meta_yml.md   |  7 ++++++
 .../_src/module_lint_tests/module_changes.md  |  6 +++++
 .../_src/module_lint_tests/module_todos.md    |  5 ++++
 docs/api/_src/pipeline_lint_tests/index.md    |  2 +-
 docs/api/make_lint_md.py                      |  9 +++----
 nf_core/lint/__init__.py                      |  8 +++----
 nf_core/modules/lint/functions_nf.py          |  9 ++++++-
 nf_core/modules/lint/main_nf.py               | 16 ++++++++++---
 nf_core/modules/lint/meta_yml.py              | 14 ++++++++++-
 nf_core/modules/lint/module_changes.py        |  7 ++++--
 nf_core/modules/lint/module_tests.py          |  9 +++++--
 nf_core/modules/lint/module_todos.py          | 24 +++++++++++++++++--
 nf_core/modules/lint/module_version.py        |  8 +++++--
 16 files changed, 122 insertions(+), 22 deletions(-)
 create mode 100644 docs/api/_src/module_lint_tests/functions_nf.md
 create mode 100644 docs/api/_src/module_lint_tests/index.md
 create mode 100644 docs/api/_src/module_lint_tests/main_nf.md
 create mode 100644 docs/api/_src/module_lint_tests/meta_yml.md
 create mode 100644 docs/api/_src/module_lint_tests/module_changes.md
 create mode 100644 docs/api/_src/module_lint_tests/module_todos.md

diff --git a/docs/api/_src/module_lint_tests/functions_nf.md b/docs/api/_src/module_lint_tests/functions_nf.md
new file mode 100644
index 0000000000..c89d1d862c
--- /dev/null
+++ b/docs/api/_src/module_lint_tests/functions_nf.md
@@ -0,0 +1,5 @@
+# functions_nf
+
+```{eval-rst}
+.. automethod:: nf_core.modules.lint.ModuleLint.functions_nf
+```
diff --git a/docs/api/_src/module_lint_tests/index.md b/docs/api/_src/module_lint_tests/index.md
new file mode 100644
index 0000000000..f889abf73c
--- /dev/null
+++ b/docs/api/_src/module_lint_tests/index.md
@@ -0,0 +1,9 @@
+# Module lint tests
+
+```{toctree}
+:caption: 'Tests:'
+:glob: true
+:maxdepth: 2
+
+*
+```
diff --git a/docs/api/_src/module_lint_tests/main_nf.md b/docs/api/_src/module_lint_tests/main_nf.md
new file mode 100644
index 0000000000..452520d705
--- /dev/null
+++ b/docs/api/_src/module_lint_tests/main_nf.md
@@ -0,0 +1,6 @@
+# main_nf
+
+```{eval-rst}
+.. automethod:: nf_core.modules.lint.ModuleLint.main_nf
+```
+
diff --git a/docs/api/_src/module_lint_tests/meta_yml.md b/docs/api/_src/module_lint_tests/meta_yml.md
new file mode 100644
index 0000000000..56e1bc8b7b
--- /dev/null
+++ b/docs/api/_src/module_lint_tests/meta_yml.md
@@ -0,0 +1,7 @@
+# meta_yml
+
+```{eval-rst}
+.. automethod:: nf_core.modules.lint.ModuleLint.meta_yml
+```
+
+    
diff --git a/docs/api/_src/module_lint_tests/module_changes.md b/docs/api/_src/module_lint_tests/module_changes.md
new file mode 100644
index 0000000000..afcd71b07b
--- /dev/null
+++ b/docs/api/_src/module_lint_tests/module_changes.md
@@ -0,0 +1,6 @@
+# module_changes
+
+```{eval-rst}
+.. automethod:: nf_core.modules.lint.ModuleLint.module_changes
+```
+
diff --git a/docs/api/_src/module_lint_tests/module_todos.md b/docs/api/_src/module_lint_tests/module_todos.md
new file mode 100644
index 0000000000..d592addd06
--- /dev/null
+++ b/docs/api/_src/module_lint_tests/module_todos.md
@@ -0,0 +1,5 @@
+# module_todos
+
+```{eval-rst}
+.. automethod:: nf_core.modules.lint.ModuleLint.module_todos
+```
diff --git a/docs/api/_src/pipeline_lint_tests/index.md b/docs/api/_src/pipeline_lint_tests/index.md
index d10f8421c5..0cf9bc1d21 100644
--- a/docs/api/_src/pipeline_lint_tests/index.md
+++ b/docs/api/_src/pipeline_lint_tests/index.md
@@ -1,4 +1,4 @@
-# Pipline lint tests
+# Pipeline lint tests
 
 ```{toctree}
 :caption: 'Tests:'
diff --git a/docs/api/make_lint_md.py b/docs/api/make_lint_md.py
index 6b54dc8682..25e5539f67 100644
--- a/docs/api/make_lint_md.py
+++ b/docs/api/make_lint_md.py
@@ -20,6 +20,7 @@ def make_docs(docs_basedir, lint_tests, md_template):
         else:
             with open(fn, "w") as fh:
                 fh.write(md_template.format(test_name))
+                print(test_name)
 
     for fn in existing_docs:
         os.remove(fn)
@@ -29,10 +30,10 @@ def make_docs(docs_basedir, lint_tests, md_template):
 pipeline_docs_basedir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "_src", "pipeline_lint_tests")
 make_docs(
     pipeline_docs_basedir,
-    nf_core.lint.PipelineLint._get_all_lint_tests(),
+    nf_core.lint.PipelineLint._get_all_lint_tests(True),
     """# {0}
 
-    ```{eval-rst}
+    ```{{eval-rst}}
     .. automethod:: nf_core.lint.PipelineLint.{0}
     ```
 
@@ -40,13 +41,13 @@ def make_docs(docs_basedir, lint_tests, md_template):
 )
 
 # Create the modules lint docs
-modules_docs_basedir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "_src", "modules_lint_tests")
+modules_docs_basedir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "_src", "module_lint_tests")
 make_docs(
     modules_docs_basedir,
     nf_core.modules.lint.ModuleLint._get_all_lint_tests(),
     """# {0}
 
-    ```{eval-rst}
+    ```{{eval-rst}}
     .. automethod:: nf_core.modules.lint.ModuleLint.{0}
     ```
 
diff --git a/nf_core/lint/__init__.py b/nf_core/lint/__init__.py
index b61765b162..1f6d8e9253 100644
--- a/nf_core/lint/__init__.py
+++ b/nf_core/lint/__init__.py
@@ -20,8 +20,8 @@
 
 import nf_core.utils
 import nf_core.lint_utils
+import nf_core.modules.lint
 from nf_core.lint_utils import console
-from nf_core.modules.lint import ModuleLint
 
 log = logging.getLogger(__name__)
 
@@ -44,7 +44,7 @@ def run_linting(
 
     # Verify that the requested tests exist
     if key:
-        all_tests = set(PipelineLint._get_all_lint_tests(release_mode)).union(set(ModuleLint._get_all_lint_tests()))
+        all_tests = set(PipelineLint._get_all_lint_tests(release_mode)).union(set(nf_core.modules.lint.ModuleLint._get_all_lint_tests()))
         bad_keys = [k for k in key if k not in all_tests]
         if len(bad_keys) > 0:
             raise AssertionError(
@@ -66,7 +66,7 @@ def run_linting(
     lint_obj._list_files()
 
     # Create the modules lint object
-    module_lint_obj = ModuleLint(pipeline_dir)
+    module_lint_obj = nf_core.modules.lint.ModuleLint(pipeline_dir)
 
     # Verify that the pipeline is correctly configured
     try:
@@ -77,7 +77,7 @@ def run_linting(
     # Run only the tests we want
     if key:
         # Select only the module lint tests
-        module_lint_tests = list(set(key).intersection(set(ModuleLint._get_all_lint_tests())))
+        module_lint_tests = list(set(key).intersection(set(nf_core.modules.lint.ModuleLint._get_all_lint_tests())))
     else:
         # If no key is supplied, run the default modules tests
         module_lint_tests = ("module_changes", "module_version")
diff --git a/nf_core/modules/lint/functions_nf.py b/nf_core/modules/lint/functions_nf.py
index 600a1ae7fd..97be84560c 100644
--- a/nf_core/modules/lint/functions_nf.py
+++ b/nf_core/modules/lint/functions_nf.py
@@ -9,7 +9,14 @@
 def functions_nf(module_lint_object, module):
     """
     Lint a functions.nf file
-    Verifies that the file exists and contains all necessary functions
+
+    Verifies that the file exists and contains the following functions::
+
+        getSoftwareName
+        initOptions
+        getPathFromList
+        saveFiles
+
     """
     local_copy = None
     template_copy = None
diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
index 018dc99af2..9fc6f63f7f 100644
--- a/nf_core/modules/lint/main_nf.py
+++ b/nf_core/modules/lint/main_nf.py
@@ -10,10 +10,20 @@
 def main_nf(module_lint_object, module):
     """
     Lint a single main.nf module file
+
     Can also be used to lint local module files,
-    in which case failures should be interpreted
-    as warnings
+    in which case failures will be reported as
+    warnings
+
+    The test checks that software versions and
+    containers are correct. It warns if that the
+    module does not have a process label or if it
+    is not among the standard ones.
+
+    In the modules script section it checks that
+    ``def software`` and ``def prefix`` are defined.
     """
+
     inputs = []
     outputs = []
 
@@ -116,7 +126,7 @@ def main_nf(module_lint_object, module):
 def check_script_section(self, lines):
     """
     Lint the script section
-    Checks whether 'def sotware' and 'def prefix' are defined
+    Checks whether 'def software' and 'def prefix' are defined
     """
     script = "".join(lines)
 
diff --git a/nf_core/modules/lint/meta_yml.py b/nf_core/modules/lint/meta_yml.py
index be265a16ec..60e4832823 100644
--- a/nf_core/modules/lint/meta_yml.py
+++ b/nf_core/modules/lint/meta_yml.py
@@ -7,7 +7,19 @@
 
 
 def meta_yml(module_lint_object, module):
-    """Lint a meta yml file"""
+    """
+    Lint a meta.yml file
+
+    The lint test checks that the module has
+    a ``meta.yml`` file and that it contains
+    the required keys: 'name', input' and
+    'output'.
+
+    In addition it checks that the module name
+    and module input is consistent between the
+    ``meta.yml`` and the ``main.nf``.
+
+    """
     required_keys = ["name", "input", "output"]
     required_keys_lists = ["input", "output"]
     try:
diff --git a/nf_core/modules/lint/module_changes.py b/nf_core/modules/lint/module_changes.py
index 57f3b9a03f..34354f1795 100644
--- a/nf_core/modules/lint/module_changes.py
+++ b/nf_core/modules/lint/module_changes.py
@@ -11,11 +11,14 @@ def module_changes(module_lint_object, module):
     """
     Checks whether installed nf-core modules have changed compared to the
     original repository
-    Downloads the 'main.nf', 'functions.nf' and 'meta.yml' files for every module
+
+    Downloads the ``main.nf``, ``functions.nf`` and ``meta.yml`` files for every module
     and compares them to the local copies
 
-    If the module has a 'git_sha', the file content is checked against this sha
+    If the module has a commit SHA entry in the ``modules.json``, the file content is
+    checked against this SHA
     """
+
     files_to_check = ["main.nf", "functions.nf", "meta.yml"]
 
     # Loop over nf-core modules
diff --git a/nf_core/modules/lint/module_tests.py b/nf_core/modules/lint/module_tests.py
index fad25d20ac..78cc18e063 100644
--- a/nf_core/modules/lint/module_tests.py
+++ b/nf_core/modules/lint/module_tests.py
@@ -3,7 +3,6 @@
 """
 import os
 import logging
-import sys
 import yaml
 
 log = logging.getLogger(__name__)
@@ -11,7 +10,13 @@
 
 def module_tests(module_lint_object, module):
     """
-    Lint module tests
+    Lint the tests of a module in nf-core/modules
+
+    It verifies that the test directory exists
+    and contains a ``main.nf`` and a ``test.yml``,
+    and that the module is present in the ``pytest_modules.yml``
+    file.
+
     """
 
     if os.path.exists(module.test_dir):
diff --git a/nf_core/modules/lint/module_todos.py b/nf_core/modules/lint/module_todos.py
index 57c73ebbcd..bbd1c4d6f7 100644
--- a/nf_core/modules/lint/module_todos.py
+++ b/nf_core/modules/lint/module_todos.py
@@ -8,8 +8,28 @@
 def module_todos(module_lint_object, module):
     """
     Look for TODO statements in the module files
-    Slight modification of the "nf_core.lint.pipeline_todos" function to make it work
-    for a single module
+
+    The nf-core module template contains a number of comment lines to help developers
+    of new modules know where they need to edit files and add content.
+    They typically have the following format:
+
+    .. code-block:: groovy
+
+        // TODO nf-core: Make some kind of change to the workflow here
+
+    ..or in markdown:
+
+    .. code-block:: html
+
+        <!-- TODO nf-core: Add some detail to the docs here -->
+
+    This lint test runs through all files in the module and searches for these lines.
+    If any are found they will throw a warning.
+
+    .. tip:: Note that many GUI code editors have plugins to list all instances of *TODO*
+              in a given project directory. This is a very quick and convenient way to get
+              started on your pipeline!
+
     """
     module.wf_path = module.module_dir
     results = pipeline_todos(module)
diff --git a/nf_core/modules/lint/module_version.py b/nf_core/modules/lint/module_version.py
index cc3e01c8be..03ea4f248c 100644
--- a/nf_core/modules/lint/module_version.py
+++ b/nf_core/modules/lint/module_version.py
@@ -18,9 +18,13 @@
 
 def module_version(module_lint_object, module):
     """
-    Verify that the module has a version (git_sha) specified in the
-    modules.json file and checks whether a new version is available
+    Verifies that the module has a version specified in the modules.json
+
+    It checks whether the module has an entry in the ``modules.json`` file
+    containing a commit SHA. If that is true, it verifies that there are no
+    newer version of the module available.
     """
+
     modules_json_path = os.path.join(module_lint_object.dir, "modules.json")
 
     # Verify that a git_sha exists in the `modules.json` file for this module

From 3bb958423a63cbd5f29a86076b271037606a11f4 Mon Sep 17 00:00:00 2001
From: Erik Danielsson <danielsson.erik.0@gmail.com>
Date: Thu, 5 Aug 2021 10:28:23 +0200
Subject: [PATCH 03/12] Small fixes

---
 nf_core/lint/modules_json.py           |  2 +-
 nf_core/modules/lint/main_nf.py        | 23 +++++++++++++----------
 nf_core/modules/lint/meta_yml.py       |  4 ++--
 nf_core/modules/lint/module_changes.py |  8 ++++----
 4 files changed, 20 insertions(+), 17 deletions(-)

diff --git a/nf_core/lint/modules_json.py b/nf_core/lint/modules_json.py
index 07abf94987..4c5923d508 100644
--- a/nf_core/lint/modules_json.py
+++ b/nf_core/lint/modules_json.py
@@ -8,7 +8,7 @@ def modules_json(self):
     """Make sure all modules described in the ``modules.json`` file are actually installed
 
     Every module installed from ``nf-core/modules`` must have an entry in the ``modules.json`` file
-    with an associated version git_sha hash.
+    with an associated version commit hash.
 
     * Failure: If module entries are found in ``modules.json`` for modules that are not installed
     """
diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
index 9fc6f63f7f..9b6d266728 100644
--- a/nf_core/modules/lint/main_nf.py
+++ b/nf_core/modules/lint/main_nf.py
@@ -13,15 +13,18 @@ def main_nf(module_lint_object, module):
 
     Can also be used to lint local module files,
     in which case failures will be reported as
-    warnings
-
-    The test checks that software versions and
-    containers are correct. It warns if that the
-    module does not have a process label or if it
-    is not among the standard ones.
-
-    In the modules script section it checks that
-    ``def software`` and ``def prefix`` are defined.
+    warnings.
+
+    The test checks for the following:
+
+    * Software versions and containers are valid
+    * The module has a process label and it is among
+      the standard ones.
+    * If a ``meta`` map is defined as one of the modules
+      inputs it should be defined as one of the outputs,
+      and be correctly configured in the ``saveAs`` function.
+    * The module script section should contain definitions
+      of ``software`` and ``prefix``
     """
 
     inputs = []
@@ -162,7 +165,7 @@ def check_process_section(self, lines):
     if all([x.upper() for x in self.process_name]):
         self.passed.append(("process_capitals", "Process name is in capital letters", self.main_nf))
     else:
-        self.failed.append(("process_capitals", "Process name is not in captial letters", self.main_nf))
+        self.failed.append(("process_capitals", "Process name is not in capital letters", self.main_nf))
 
     # Check that process labels are correct
     correct_process_labels = ["process_low", "process_medium", "process_high", "process_long"]
diff --git a/nf_core/modules/lint/meta_yml.py b/nf_core/modules/lint/meta_yml.py
index 60e4832823..561f230c91 100644
--- a/nf_core/modules/lint/meta_yml.py
+++ b/nf_core/modules/lint/meta_yml.py
@@ -12,8 +12,8 @@ def meta_yml(module_lint_object, module):
 
     The lint test checks that the module has
     a ``meta.yml`` file and that it contains
-    the required keys: 'name', input' and
-    'output'.
+    the required keys: ``name``, input`` and
+    ``output``.
 
     In addition it checks that the module name
     and module input is consistent between the
diff --git a/nf_core/modules/lint/module_changes.py b/nf_core/modules/lint/module_changes.py
index 34354f1795..b75b2e0067 100644
--- a/nf_core/modules/lint/module_changes.py
+++ b/nf_core/modules/lint/module_changes.py
@@ -10,13 +10,13 @@
 def module_changes(module_lint_object, module):
     """
     Checks whether installed nf-core modules have changed compared to the
-    original repository
+    original repository.
 
-    Downloads the ``main.nf``, ``functions.nf`` and ``meta.yml`` files for every module
-    and compares them to the local copies
+    Downloads the ``main.nf``, ``functions.nf`` and ``meta.yml`` files from the remote
+    for every module and compares them to the local copies.
 
     If the module has a commit SHA entry in the ``modules.json``, the file content is
-    checked against this SHA
+    compared against the files in the remote at this SHA.
     """
 
     files_to_check = ["main.nf", "functions.nf", "meta.yml"]

From fee0040a9a25a07de6f431e43185d40e87010627 Mon Sep 17 00:00:00 2001
From: Erik Danielsson <danielsson.erik.0@gmail.com>
Date: Thu, 5 Aug 2021 10:33:37 +0200
Subject: [PATCH 04/12] Minor changes

---
 nf_core/modules/lint/functions_nf.py   | 2 +-
 nf_core/modules/lint/main_nf.py        | 2 +-
 nf_core/modules/lint/meta_yml.py       | 2 +-
 nf_core/modules/lint/module_tests.py   | 2 +-
 nf_core/modules/lint/module_version.py | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/nf_core/modules/lint/functions_nf.py b/nf_core/modules/lint/functions_nf.py
index 97be84560c..f927e55ffc 100644
--- a/nf_core/modules/lint/functions_nf.py
+++ b/nf_core/modules/lint/functions_nf.py
@@ -8,7 +8,7 @@
 
 def functions_nf(module_lint_object, module):
     """
-    Lint a functions.nf file
+    Lint a ``functions.nf`` file
 
     Verifies that the file exists and contains the following functions::
 
diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
index 9b6d266728..555fcedc5a 100644
--- a/nf_core/modules/lint/main_nf.py
+++ b/nf_core/modules/lint/main_nf.py
@@ -9,7 +9,7 @@
 
 def main_nf(module_lint_object, module):
     """
-    Lint a single main.nf module file
+    Lint a ``main.nf`` module file
 
     Can also be used to lint local module files,
     in which case failures will be reported as
diff --git a/nf_core/modules/lint/meta_yml.py b/nf_core/modules/lint/meta_yml.py
index 561f230c91..3c59c774d4 100644
--- a/nf_core/modules/lint/meta_yml.py
+++ b/nf_core/modules/lint/meta_yml.py
@@ -8,7 +8,7 @@
 
 def meta_yml(module_lint_object, module):
     """
-    Lint a meta.yml file
+    Lint a ``meta.yml`` file
 
     The lint test checks that the module has
     a ``meta.yml`` file and that it contains
diff --git a/nf_core/modules/lint/module_tests.py b/nf_core/modules/lint/module_tests.py
index 78cc18e063..f76d45d69f 100644
--- a/nf_core/modules/lint/module_tests.py
+++ b/nf_core/modules/lint/module_tests.py
@@ -10,7 +10,7 @@
 
 def module_tests(module_lint_object, module):
     """
-    Lint the tests of a module in nf-core/modules
+    Lint the tests of a module in ``nf-core/modules``
 
     It verifies that the test directory exists
     and contains a ``main.nf`` and a ``test.yml``,
diff --git a/nf_core/modules/lint/module_version.py b/nf_core/modules/lint/module_version.py
index 03ea4f248c..29d7327490 100644
--- a/nf_core/modules/lint/module_version.py
+++ b/nf_core/modules/lint/module_version.py
@@ -18,7 +18,7 @@
 
 def module_version(module_lint_object, module):
     """
-    Verifies that the module has a version specified in the modules.json
+    Verifies that the module has a version specified in the ``modules.json`` file
 
     It checks whether the module has an entry in the ``modules.json`` file
     containing a commit SHA. If that is true, it verifies that there are no

From 2aad12159eb34132572aac0baba3e54e0ec88f50 Mon Sep 17 00:00:00 2001
From: Erik Danielsson <danielsson.erik.0@gmail.com>
Date: Thu, 5 Aug 2021 10:50:06 +0200
Subject: [PATCH 05/12] run markdownlint

---
 docs/api/_src/module_lint_tests/main_nf.md        | 1 -
 docs/api/_src/module_lint_tests/meta_yml.md       | 2 --
 docs/api/_src/module_lint_tests/module_changes.md | 1 -
 3 files changed, 4 deletions(-)

diff --git a/docs/api/_src/module_lint_tests/main_nf.md b/docs/api/_src/module_lint_tests/main_nf.md
index 452520d705..5a96785733 100644
--- a/docs/api/_src/module_lint_tests/main_nf.md
+++ b/docs/api/_src/module_lint_tests/main_nf.md
@@ -3,4 +3,3 @@
 ```{eval-rst}
 .. automethod:: nf_core.modules.lint.ModuleLint.main_nf
 ```
-
diff --git a/docs/api/_src/module_lint_tests/meta_yml.md b/docs/api/_src/module_lint_tests/meta_yml.md
index 56e1bc8b7b..33920a4b9b 100644
--- a/docs/api/_src/module_lint_tests/meta_yml.md
+++ b/docs/api/_src/module_lint_tests/meta_yml.md
@@ -3,5 +3,3 @@
 ```{eval-rst}
 .. automethod:: nf_core.modules.lint.ModuleLint.meta_yml
 ```
-
-    
diff --git a/docs/api/_src/module_lint_tests/module_changes.md b/docs/api/_src/module_lint_tests/module_changes.md
index afcd71b07b..ce2d428ca9 100644
--- a/docs/api/_src/module_lint_tests/module_changes.md
+++ b/docs/api/_src/module_lint_tests/module_changes.md
@@ -3,4 +3,3 @@
 ```{eval-rst}
 .. automethod:: nf_core.modules.lint.ModuleLint.module_changes
 ```
-

From 1ea015e68fa1e4e92526373fe582998a48106817 Mon Sep 17 00:00:00 2001
From: Erik Danielsson <danielsson.erik.0@gmail.com>
Date: Thu, 5 Aug 2021 10:57:46 +0200
Subject: [PATCH 06/12] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7f37986284..cc296788a5 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,7 @@
 
 * Changed `questionary` `ask()` to `unsafe_ask()` to not catch `KeyboardInterupts` ([#1237](https://github.com/nf-core/tools/issues/1237))
 * Convert documentation to MyST.
+* Add documentation for the `nf-core modules lint` tests.
 
 ### Modules
 

From d3f1b85035d612d15e719f08eec1f8d7d5bae874 Mon Sep 17 00:00:00 2001
From: Erik Danielsson <danielsson.erik.0@gmail.com>
Date: Thu, 5 Aug 2021 11:05:21 +0200
Subject: [PATCH 07/12] Fix issues in md templates

---
 docs/api/make_lint_md.py | 18 ++++++++----------
 1 file changed, 8 insertions(+), 10 deletions(-)

diff --git a/docs/api/make_lint_md.py b/docs/api/make_lint_md.py
index 25e5539f67..a6ec98a944 100644
--- a/docs/api/make_lint_md.py
+++ b/docs/api/make_lint_md.py
@@ -33,11 +33,10 @@ def make_docs(docs_basedir, lint_tests, md_template):
     nf_core.lint.PipelineLint._get_all_lint_tests(True),
     """# {0}
 
-    ```{{eval-rst}}
-    .. automethod:: nf_core.lint.PipelineLint.{0}
-    ```
-
-    """,
+```{{eval-rst}}
+.. automethod:: nf_core.lint.PipelineLint.{0}
+```
+""",
 )
 
 # Create the modules lint docs
@@ -47,9 +46,8 @@ def make_docs(docs_basedir, lint_tests, md_template):
     nf_core.modules.lint.ModuleLint._get_all_lint_tests(),
     """# {0}
 
-    ```{{eval-rst}}
-    .. automethod:: nf_core.modules.lint.ModuleLint.{0}
-    ```
-
-    """,
+```{{eval-rst}}
+.. automethod:: nf_core.modules.lint.ModuleLint.{0}
+```
+""",
 )

From 1b151d22ecb4caf5bf58c6aa690ff04ee506261d Mon Sep 17 00:00:00 2001
From: Erik Danielsson <danielsson.erik.0@gmail.com>
Date: Thu, 5 Aug 2021 11:08:28 +0200
Subject: [PATCH 08/12] black

---
 nf_core/lint/__init__.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/nf_core/lint/__init__.py b/nf_core/lint/__init__.py
index 1f6d8e9253..4838726928 100644
--- a/nf_core/lint/__init__.py
+++ b/nf_core/lint/__init__.py
@@ -44,7 +44,9 @@ def run_linting(
 
     # Verify that the requested tests exist
     if key:
-        all_tests = set(PipelineLint._get_all_lint_tests(release_mode)).union(set(nf_core.modules.lint.ModuleLint._get_all_lint_tests()))
+        all_tests = set(PipelineLint._get_all_lint_tests(release_mode)).union(
+            set(nf_core.modules.lint.ModuleLint._get_all_lint_tests())
+        )
         bad_keys = [k for k in key if k not in all_tests]
         if len(bad_keys) > 0:
             raise AssertionError(

From 0926f0395d68f16e13b5677ef4ae53676f2161e3 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Wed, 16 Mar 2022 15:57:36 +0100
Subject: [PATCH 09/12] Fix github wf variable names in deploy workflow

---
 .github/workflows/tools-api-docs-dev.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/tools-api-docs-dev.yml b/.github/workflows/tools-api-docs-dev.yml
index 8a45922c7c..34feec23f1 100644
--- a/.github/workflows/tools-api-docs-dev.yml
+++ b/.github/workflows/tools-api-docs-dev.yml
@@ -27,7 +27,7 @@ jobs:
 
       - name: Sync dev docs
         # Only sync with the website if it was a push from nf-core/tools dev branch
-        if: github.repository == 'nf-core/tools' && github.event.type == 'push' && github.event.base_ref == 'refs/heads/dev'
+        if: github.repository == 'nf-core/tools' && github.event_name == 'push' && github.event.ref == 'refs/heads/dev'
         uses: SamKirkland/FTP-Deploy-Action@4.0.0
         with:
           server: ${{ secrets.ftp_server }}

From 21d1b4fe881df8c20ea77a95a2b5d725976b9152 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Wed, 16 Mar 2022 16:08:38 +0100
Subject: [PATCH 10/12] Remove sphinx scaffold page for old functions_nf.md

---
 docs/api/_src/module_lint_tests/functions_nf.md | 5 -----
 1 file changed, 5 deletions(-)
 delete mode 100644 docs/api/_src/module_lint_tests/functions_nf.md

diff --git a/docs/api/_src/module_lint_tests/functions_nf.md b/docs/api/_src/module_lint_tests/functions_nf.md
deleted file mode 100644
index c89d1d862c..0000000000
--- a/docs/api/_src/module_lint_tests/functions_nf.md
+++ /dev/null
@@ -1,5 +0,0 @@
-# functions_nf
-
-```{eval-rst}
-.. automethod:: nf_core.modules.lint.ModuleLint.functions_nf
-```

From c3224a6429b50254bb27024a9347c369726b1a5c Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Wed, 16 Mar 2022 16:11:37 +0100
Subject: [PATCH 11/12] Ran make_lint_md.py

---
 docs/api/_src/module_lint_tests/module_changes.md      | 5 -----
 docs/api/_src/module_lint_tests/module_deprecations.md | 5 +++++
 2 files changed, 5 insertions(+), 5 deletions(-)
 delete mode 100644 docs/api/_src/module_lint_tests/module_changes.md
 create mode 100644 docs/api/_src/module_lint_tests/module_deprecations.md

diff --git a/docs/api/_src/module_lint_tests/module_changes.md b/docs/api/_src/module_lint_tests/module_changes.md
deleted file mode 100644
index ce2d428ca9..0000000000
--- a/docs/api/_src/module_lint_tests/module_changes.md
+++ /dev/null
@@ -1,5 +0,0 @@
-# module_changes
-
-```{eval-rst}
-.. automethod:: nf_core.modules.lint.ModuleLint.module_changes
-```
diff --git a/docs/api/_src/module_lint_tests/module_deprecations.md b/docs/api/_src/module_lint_tests/module_deprecations.md
new file mode 100644
index 0000000000..f00b4dc54d
--- /dev/null
+++ b/docs/api/_src/module_lint_tests/module_deprecations.md
@@ -0,0 +1,5 @@
+# module_deprecations
+
+```{eval-rst}
+.. automethod:: nf_core.modules.lint.ModuleLint.module_deprecations
+```

From 01597b7ca0cab3fb92ff124217794a60acf25ca7 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Wed, 16 Mar 2022 16:24:27 +0100
Subject: [PATCH 12/12] Fix broken links

---
 docs/api/_src/api/lint.md |  2 +-
 docs/api/_src/index.md    | 10 ++++------
 2 files changed, 5 insertions(+), 7 deletions(-)

diff --git a/docs/api/_src/api/lint.md b/docs/api/_src/api/lint.md
index a0e3a6d5c9..cb75b0ecb5 100644
--- a/docs/api/_src/api/lint.md
+++ b/docs/api/_src/api/lint.md
@@ -1,7 +1,7 @@
 # nf_core.lint
 
 :::{seealso}
-See the [Lint Tests](../lint_tests/index.html) docs for information about specific linting functions.
+See the [Lint Tests](../pipeline_lint_tests/index.md) docs for information about specific linting functions.
 :::
 
 ```{eval-rst}
diff --git a/docs/api/_src/index.md b/docs/api/_src/index.md
index a6fb767122..de39e7244b 100644
--- a/docs/api/_src/index.md
+++ b/docs/api/_src/index.md
@@ -13,12 +13,10 @@ api/index.rst
 
 This documentation is for the `nf-core/tools` package.
 
-Primarily, it describes the different [code lint tests](lint_tests/index.html)
-run by `nf-core lint` (typically visited by a developer when their pipeline fails a given
-test), and also reference for the `nf_core` [Python package API](api/index.html).
-
-## Indices and tables
+## Contents
 
+- [Pipeline code lint tests](pipeline_lint_tests/index.md) (run by `nf-core lint`)
+- [Module code lint tests](module_lint_tests/index.md) (run by `nf-core modules lint`)
+- [nf-core/tools Python package API reference](api/index.md)
 - {ref}`genindex`
 - {ref}`modindex`
-- {ref}`search`