From 5ee9af351e514dc3c0ce552c49519dab3f037ed9 Mon Sep 17 00:00:00 2001
From: Erik Danielsson <danielsson.erik.0@gmail.com>
Date: Tue, 6 Jul 2021 11:48:34 +0200
Subject: [PATCH 01/11] Typos and replace duplicated functions

---
 nf_core/modules/lint/__init__.py | 170 +++++++++++++++----------------
 nf_core/modules/nfcore_module.py |   4 +-
 2 files changed, 86 insertions(+), 88 deletions(-)

diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py
index f9762569f7..a6926ccdbc 100644
--- a/nf_core/modules/lint/__init__.py
+++ b/nf_core/modules/lint/__init__.py
@@ -176,85 +176,31 @@ def lint(self, module=None, all_modules=False, print_results=True, show_passed=F
                         self.lint_tests.remove(test_name)
 
         # Lint local modules
+        print(local_modules)
         if local and len(local_modules) > 0:
-            self.lint_local_modules(local_modules)
+            self.lint_modules(local_modules, local=True)
 
         # Lint nf-core modules
         if len(nfcore_modules) > 0:
-            self.lint_nfcore_modules(nfcore_modules)
+            self.lint_modules(nfcore_modules, local=False)
 
         if print_results:
             self._print_results(show_passed=show_passed)
 
         return {"passed": self.passed, "warned": self.warned, "failed": self.failed}
 
-    def lint_local_modules(self, local_modules):
-        """
-        Lint a local module
-        Only issues warnings instead of failures
-        """
-        progress_bar = rich.progress.Progress(
-            "[bold blue]{task.description}",
-            rich.progress.BarColumn(bar_width=None),
-            "[magenta]{task.completed} of {task.total}[reset] » [bold yellow]{task.fields[test_name]}",
-            transient=True,
-        )
-        with progress_bar:
-            lint_progress = progress_bar.add_task(
-                "Linting local modules", total=len(local_modules), test_name=os.path.basename(local_modules[0])
-            )
-
-            for mod in local_modules:
-                progress_bar.update(lint_progress, advance=1, test_name=os.path.basename(mod))
-                mod_object = NFCoreModule(
-                    module_dir=mod, base_dir=self.dir, repo_type=self.repo_type, nf_core_module=False
-                )
-                mod_object.main_nf = mod
-                mod_object.module_name = os.path.basename(mod)
-                self.lint_module(mod_object, local=True)
-
-    def lint_nfcore_modules(self, nfcore_modules):
-        """
-        Lint nf-core modules
-        For each nf-core module, checks for existence of the files
-        - main.nf
-        - meta.yml
-        - functions.nf
-        And verifies that their content.
-
-        If the linting is run for modules in the central nf-core/modules repo
-        (repo_type==modules), files that are relevant for module testing are
-        also examined
-        """
-
-        progress_bar = rich.progress.Progress(
-            "[bold blue]{task.description}",
-            rich.progress.BarColumn(bar_width=None),
-            "[magenta]{task.completed} of {task.total}[reset] » [bold yellow]{task.fields[test_name]}",
-            transient=True,
-        )
-        with progress_bar:
-            lint_progress = progress_bar.add_task(
-                "Linting nf-core modules", total=len(nfcore_modules), test_name=nfcore_modules[0].module_name
-            )
-            for mod in nfcore_modules:
-                progress_bar.update(lint_progress, advance=1, test_name=mod.module_name)
-                self.lint_module(mod)
-
     def get_installed_modules(self):
         """
-        Make a list of all modules installed in this repository
+        Makes lists of the local and and nf-core modules installed in this directory.
 
-        Returns a tuple of two lists, one for local modules
-        and one for nf-core modules. The local modules are represented
-        as direct filepaths to the module '.nf' file.
-        Nf-core module are returned as file paths to the module directories.
-        In case the module contains several tools, one path to each tool directory
-        is returned.
+        Returns:
+            local_modules, nfcore_modules ([NfCoreModule], [NfCoreModule]):
+                A tuple of two lists: One for local modules and one for nf-core modules.
+                In case the module contains several subtools, one path to each tool directory
+                is returned.
 
-        returns (local_modules, nfcore_modules)
         """
-        # initialize lists
+        # Initialize lists
         local_modules = []
         nfcore_modules = []
         local_modules_dir = None
@@ -262,7 +208,7 @@ def get_installed_modules(self):
 
         # Get local modules
         if self.repo_type == "pipeline":
-            local_modules_dir = os.path.join(self.dir, "modules", "local", "process")
+            local_modules_dir = os.path.join(self.dir, "modules", "local")
 
             # Filter local modules
             if os.path.exists(local_modules_dir):
@@ -288,15 +234,86 @@ def get_installed_modules(self):
                 else:
                     nfcore_modules.append(m)
 
-        # Make full (relative) file paths and create NFCoreModule objects
-        local_modules = [os.path.join(local_modules_dir, m) for m in local_modules]
+        # Create NFCoreModule objects for the nf-core and local modules
         nfcore_modules = [
             NFCoreModule(os.path.join(nfcore_modules_dir, m), repo_type=self.repo_type, base_dir=self.dir)
             for m in nfcore_modules
         ]
 
+        local_modules = [
+            NFCoreModule(
+                os.path.join(local_modules_dir, m), repo_type=self.repo_type, base_dir=self.dir, nf_core_module=False
+            )
+            for m in local_modules
+        ]
+
+        # The local modules mustn't conform to the same file structure
+        # as the nf-core modules. We therefore only check the main script
+        # of the module
+        for mod in local_modules:
+            mod.main_nf = mod.module_dir
+            mod.module_name = os.path.basename(mod.module_dir)
+
         return local_modules, nfcore_modules
 
+    def lint_modules(self, modules, local=False):
+        """
+        Lint a list of modules
+
+        Args:
+            modules ([NFCoreModule]): A list of module objects
+            local (boolean): Whether the list consist of local or nf-core modules
+        """
+        progress_bar = rich.progress.Progress(
+            "[bold blue]{task.description}",
+            rich.progress.BarColumn(bar_width=None),
+            "[magenta]{task.completed} of {task.total}[reset] » [bold yellow]{task.fields[test_name]}",
+            transient=True,
+        )
+        with progress_bar:
+            lint_progress = progress_bar.add_task(
+                f"Linting {'local' if local else 'nf-core'} modules",
+                total=len(modules),
+                test_name=modules[0].module_name,
+            )
+
+            for mod in modules:
+                progress_bar.update(lint_progress, advance=1, test_name=mod.module_name)
+                self.lint_module(mod, local=local)
+
+    def lint_module(self, mod, local=False):
+        """
+        Perform linting on one module
+
+        If the module is a local module we only check the `main.nf` file,
+        and it issue warnings instead of failures.
+
+        If the module is a nf-core module we check for existence of the files
+        - main.nf
+        - meta.yml
+        - functions.nf
+        And verify that their content conform to the nf-core standards.
+
+        If the linting is run for modules in the central nf-core/modules repo
+        (repo_type==modules), files that are relevant for module testing are
+        also examined
+        """
+
+        # Only check the main script in case of a local module
+        if local:
+            self.main_nf(mod)
+            self.passed += [LintResult(mod, *m) for m in mod.passed]
+            self.warned += [LintResult(mod, *m) for m in mod.warned]
+
+        # Otherwise run all the lint tests
+        else:
+            for test_name in self.lint_tests:
+                getattr(self, test_name)(mod)
+
+            self.passed += [LintResult(mod, *m) for m in mod.passed]
+            self.warned += [LintResult(mod, *m) for m in mod.warned]
+            self.failed += [LintResult(mod, *m) for m in mod.failed]
+
     def _print_results(self, show_passed=False):
         """Print linting results to the command line.
 
@@ -399,22 +416,3 @@ def _s(some_list):
         table.add_row(r"[!] {:>3} Test Warning{}".format(len(self.warned), _s(self.warned)), style="yellow")
         table.add_row(r"[✗] {:>3} Test{} Failed".format(len(self.failed), _s(self.failed)), style="red")
         console.print(table)
-
-    def lint_module(self, mod, local=False):
-        """Perform linting on this module"""
-        # Iterate over modules and run all checks on them
-
-        # Only check main_if in case of a local module
-        if local:
-            self.main_nf(mod)
-            self.passed += [LintResult(mod, m[0], m[1], m[2]) for m in mod.passed]
-            self.warned += [LintResult(mod, m[0], m[1], m[2]) for m in mod.warned]
-
-        # Otherwise run all the lint tests
-        else:
-            for test_name in self.lint_tests:
-                getattr(self, test_name)(mod)
-
-            self.passed += [LintResult(mod, m[0], m[1], m[2]) for m in mod.passed]
-            self.warned += [LintResult(mod, m[0], m[1], m[2]) for m in mod.warned]
-            self.failed += [LintResult(mod, m[0], m[1], m[2]) for m in mod.failed]
diff --git a/nf_core/modules/nfcore_module.py b/nf_core/modules/nfcore_module.py
index 28939579e0..9eb3feee56 100644
--- a/nf_core/modules/nfcore_module.py
+++ b/nf_core/modules/nfcore_module.py
@@ -1,12 +1,12 @@
 """
-The NFCoreModule class holds information and uitily functions for a single module
+The NFCoreModule class holds information and utility functions for a single module
 """
 import os
 
 
 class NFCoreModule(object):
     """
-    A class to hold the information a bout a nf-core module
+    A class to hold the information about a nf-core module
     Includes functionality for linting
     """
 

From 0050c75739aa3ad126fb33b1b4ee188ec360be7d Mon Sep 17 00:00:00 2001
From: Erik Danielsson <danielsson.erik.0@gmail.com>
Date: Tue, 6 Jul 2021 14:32:17 +0200
Subject: [PATCH 02/11] Break up code into functions

---
 nf_core/modules/lint/__init__.py | 91 ++++++++++++++++++--------------
 1 file changed, 51 insertions(+), 40 deletions(-)

diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py
index a6926ccdbc..fb0fd25069 100644
--- a/nf_core/modules/lint/__init__.py
+++ b/nf_core/modules/lint/__init__.py
@@ -108,29 +108,33 @@ def lint(self, module=None, all_modules=False, print_results=True, show_passed=F
         :param print_results:   Whether to print the linting results
         :param show_passed:     Whether passed tests should be shown as well
 
-        :returns:               dict of {passed, warned, failed}
+        :returns:               A ModuleLint object containing information of
+                                the passed, warned and failed tests
         """
 
-        # Get list of all modules in a pipeline
+        # Get lists of all modules in a pipeline
         local_modules, nfcore_modules = self.get_installed_modules()
 
         # Prompt for module or all
         if module is None and not all_modules:
-            question = {
-                "type": "list",
-                "name": "all_modules",
-                "message": "Lint all modules or a single named module?",
-                "choices": ["All modules", "Named module"],
-            }
-            answer = questionary.unsafe_prompt([question], style=nf_core.utils.nfcore_question_style)
-            if answer["all_modules"] == "All modules":
-                all_modules = True
-            else:
-                module = questionary.autocomplete(
-                    "Tool name:",
-                    choices=[m.module_name for m in nfcore_modules],
-                    style=nf_core.utils.nfcore_question_style,
-                ).ask()
+            questions = [
+                {
+                    "type": "list",
+                    "name": "all_modules",
+                    "message": "Lint all modules or a single named module?",
+                    "choices": ["All modules", "Named module"],
+                },
+                {
+                    "type": "autocomplete",
+                    "name": "tool_name",
+                    "message": "Tool name:",
+                    "when": lambda x: x["all_modules"] == "Named module",
+                    "choices": [m.module_name for m in nfcore_modules],
+                },
+            ]
+            answers = questionary.unsafe_prompt(questions, style=nf_core.utils.nfcore_question_style)
+            all_modules = answers["all_modules"] == "All modules"
+            module = answers.get("tool_name")
 
         # Only lint the given module
         if module:
@@ -148,35 +152,16 @@ def lint(self, module=None, all_modules=False, print_results=True, show_passed=F
         if module:
             log.info(f"Linting module: [magenta]{module}")
 
-        # Check that supplied test keys exist
-        bad_keys = [k for k in self.key if k not in self.lint_tests]
-        if len(bad_keys) > 0:
-            raise AssertionError(
-                "Test name{} not recognised: '{}'".format(
-                    "s" if len(bad_keys) > 1 else "",
-                    "', '".join(bad_keys),
-                )
-            )
-
-        # If -k supplied, only run these tests
+        # Filter the tests by the key if one is supplied
         if self.key:
+            self.filter_tests_by_key()
             log.info("Only running tests: '{}'".format("', '".join(self.key)))
-            self.lint_tests = [k for k in self.lint_tests if k in self.key]
 
         # If it is a pipeline, load the lint config file and the modules.json file
         if self.repo_type == "pipeline":
-            self.load_lint_config()
-            self.modules_json = self.load_modules_json()
-
-            # Only continue if a lint config has been loaded
-            if self.lint_config:
-                for test_name in self.lint_tests:
-                    if self.lint_config.get(test_name, {}) is False:
-                        log.info(f"Ignoring lint test: {test_name}")
-                        self.lint_tests.remove(test_name)
+            self.set_up_pipeline_files()
 
         # Lint local modules
-        print(local_modules)
         if local and len(local_modules) > 0:
             self.lint_modules(local_modules, local=True)
 
@@ -187,7 +172,33 @@ def lint(self, module=None, all_modules=False, print_results=True, show_passed=F
         if print_results:
             self._print_results(show_passed=show_passed)
 
-        return {"passed": self.passed, "warned": self.warned, "failed": self.failed}
+        return self
+
+    def set_up_pipeline_files(self):
+        self.load_lint_config()
+        self.modules_json = self.load_modules_json()
+
+        # Only continue if a lint config has been loaded
+        if self.lint_config:
+            for test_name in self.lint_tests:
+                if self.lint_config.get(test_name, {}) is False:
+                    log.info(f"Ignoring lint test: {test_name}")
+                    self.lint_tests.remove(test_name)
+
+    def filter_tests_by_key(self):
+        """Filters the tests by the supplied key"""
+        # Check that supplied test keys exist
+        bad_keys = [k for k in self.key if k not in self.lint_tests]
+        if len(bad_keys) > 0:
+            raise AssertionError(
+                "Test name{} not recognised: '{}'".format(
+                    "s" if len(bad_keys) > 1 else "",
+                    "', '".join(bad_keys),
+                )
+            )
+
+        # If -k supplied, only run these tests
+        self.lint_tests = [k for k in self.lint_tests if k in self.key]
 
     def get_installed_modules(self):
         """

From 4497775b571d6f98475adc85cba661c952bae5e6 Mon Sep 17 00:00:00 2001
From: Erik Danielsson <danielsson.erik.0@gmail.com>
Date: Tue, 6 Jul 2021 14:51:43 +0200
Subject: [PATCH 03/11] Clean up code

---
 nf_core/modules/lint/__init__.py | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py
index fb0fd25069..fbc91c469c 100644
--- a/nf_core/modules/lint/__init__.py
+++ b/nf_core/modules/lint/__init__.py
@@ -78,6 +78,10 @@ def __init__(self, dir, key=()):
         self.failed = []
         self.modules_repo = ModulesRepo()
         self.lint_tests = ["main_nf", "functions_nf", "meta_yml", "module_changes", "module_todos"]
+
+        # Get lists of modules install in directory
+        self.all_local_modules, self.all_nfcore_modules = self.get_installed_modules()
+
         self.key = key
         self.lint_config = None
         self.modules_json = None
@@ -112,9 +116,6 @@ def lint(self, module=None, all_modules=False, print_results=True, show_passed=F
                                 the passed, warned and failed tests
         """
 
-        # Get lists of all modules in a pipeline
-        local_modules, nfcore_modules = self.get_installed_modules()
-
         # Prompt for module or all
         if module is None and not all_modules:
             questions = [
@@ -129,7 +130,7 @@ def lint(self, module=None, all_modules=False, print_results=True, show_passed=F
                     "name": "tool_name",
                     "message": "Tool name:",
                     "when": lambda x: x["all_modules"] == "Named module",
-                    "choices": [m.module_name for m in nfcore_modules],
+                    "choices": [m.module_name for m in self.all_nfcore_modules],
                 },
             ]
             answers = questionary.unsafe_prompt(questions, style=nf_core.utils.nfcore_question_style)
@@ -141,9 +142,12 @@ def lint(self, module=None, all_modules=False, print_results=True, show_passed=F
             if all_modules:
                 raise ModuleLintException("You cannot specify a tool and request all tools to be linted.")
             local_modules = []
-            nfcore_modules = [m for m in nfcore_modules if m.module_name == module]
+            nfcore_modules = [m for m in self.all_nfcore_modules if m.module_name == module]
             if len(nfcore_modules) == 0:
                 raise ModuleLintException(f"Could not find the specified module: '{module}'")
+        else:
+            local_modules = self.all_local_modules
+            nfcore_modules = self.all_nfcore_modules
 
         if self.repo_type == "modules":
             log.info(f"Linting modules repo: [magenta]{self.dir}")
@@ -172,8 +176,6 @@ def lint(self, module=None, all_modules=False, print_results=True, show_passed=F
         if print_results:
             self._print_results(show_passed=show_passed)
 
-        return self
-
     def set_up_pipeline_files(self):
         self.load_lint_config()
         self.modules_json = self.load_modules_json()

From a0f9a3a62f7c589c8da47855d9eb2bad0190afb8 Mon Sep 17 00:00:00 2001
From: Erik Danielsson <danielsson.erik.0@gmail.com>
Date: Tue, 6 Jul 2021 16:08:21 +0200
Subject: [PATCH 04/11] Add header to lint results table and joint summary

---
 nf_core/__main__.py              |  6 ++--
 nf_core/lint/__init__.py         | 61 +++++++++++++++++++++++---------
 nf_core/lint_utils.py            | 32 +++++++++++++++++
 nf_core/modules/lint/__init__.py | 28 ++++++++++-----
 4 files changed, 101 insertions(+), 26 deletions(-)
 create mode 100644 nf_core/lint_utils.py

diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index fbce259f27..b702a4b6cb 100755
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -333,8 +333,10 @@ def lint(dir, release, fix, key, show_passed, fail_ignored, markdown, json):
 
     # Run the lint tests!
     try:
-        lint_obj = nf_core.lint.run_linting(dir, release, fix, key, show_passed, fail_ignored, markdown, json)
-        if len(lint_obj.failed) > 0:
+        lint_obj, module_lint_obj = nf_core.lint.run_linting(
+            dir, release, fix, key, show_passed, fail_ignored, markdown, json
+        )
+        if len(lint_obj.failed) + len(module_lint_obj.failed) > 0:
             sys.exit(1)
     except AssertionError as e:
         log.critical(e)
diff --git a/nf_core/lint/__init__.py b/nf_core/lint/__init__.py
index b53e0ae6d7..69eac9e6e0 100644
--- a/nf_core/lint/__init__.py
+++ b/nf_core/lint/__init__.py
@@ -8,6 +8,7 @@
 from rich.console import Console
 from rich.markdown import Markdown
 from rich.table import Table
+from rich.panel import Panel
 import datetime
 import git
 import json
@@ -19,6 +20,8 @@
 import yaml
 
 import nf_core.utils
+import nf_core.lint_utils
+from nf_core.modules.lint import ModuleLint
 
 log = logging.getLogger(__name__)
 
@@ -40,7 +43,7 @@ def run_linting(
     """
 
     # Create the lint object
-    lint_obj = PipelineLint(pipeline_dir, release_mode, fix, key, fail_ignored)
+    lint_obj = PipelineLint(pipeline_dir, release_mode, fix, key, fail_ignored, show_passed)
 
     # Load the various pipeline configs
     lint_obj._load_lint_config()
@@ -48,16 +51,31 @@ def run_linting(
     lint_obj._load_conda_environment()
     lint_obj._list_files()
 
-    # Run the linting tests
+    # Create the modules lint object
+    module_lint_obj = ModuleLint(pipeline_dir)
+
+    # Run only the tests we want
+    module_lint_tests = ("module_changes",)
+    module_lint_obj.filter_tests_by_key(module_lint_tests)
+
+    # Run the pipeline linting tests
     try:
         lint_obj._lint_pipeline()
     except AssertionError as e:
         log.critical("Critical error: {}".format(e))
         log.info("Stopping tests...")
-        return lint_obj
+        return lint_obj, module_lint_obj
+
+    # Run the module lint tests
+    if len(module_lint_obj.all_local_modules) > 0:
+        module_lint_obj.lint_modules(module_lint_obj.all_local_modules, local=True)
+    if len(module_lint_obj.all_nfcore_modules) > 0:
+        module_lint_obj.lint_modules(module_lint_obj.all_nfcore_modules, local=False)
 
     # Print the results
     lint_obj._print_results(show_passed)
+    module_lint_obj._print_results(show_passed)
+    nf_core.lint_utils.print_joint_summary(lint_obj, module_lint_obj)
 
     # Save results to Markdown file
     if md_fn is not None:
@@ -75,7 +93,7 @@ def run_linting(
         if release_mode:
             log.info("Reminder: Lint tests were run in --release mode.")
 
-    return lint_obj
+    return lint_obj, module_lint_obj
 
 
 class PipelineLint(nf_core.utils.Pipeline):
@@ -117,7 +135,7 @@ class PipelineLint(nf_core.utils.Pipeline):
     from .template_strings import template_strings
     from .version_consistency import version_consistency
 
-    def __init__(self, wf_path, release_mode=False, fix=(), key=(), fail_ignored=False):
+    def __init__(self, wf_path, release_mode=False, fix=(), key=(), fail_ignored=False, show_passed=False):
         """Initialise linting object"""
 
         # Initialise the parent object
@@ -280,7 +298,7 @@ def _lint_pipeline(self):
                 if test_results.get("could_fix", False):
                     self.could_fix.append(test_name)
 
-    def _print_results(self, show_passed=False):
+    def _print_results(self, show_passed):
         """Print linting results to the command line.
 
         Uses the ``rich`` library to print a set of formatted tables to the command line
@@ -305,6 +323,9 @@ def _s(some_list):
                 return "s"
             return ""
 
+        # Print lint results header
+        console.print(Panel("[magenta]General lint results"))
+
         # Table of passed tests
         if len(self.passed) > 0 and show_passed:
             table = Table(style="green", box=rich.box.ROUNDED)
@@ -340,6 +361,24 @@ def _s(some_list):
             table = format_result(self.failed, table)
             console.print(table)
 
+        if len(self.could_fix):
+            fix_cmd = "nf-core lint {} --fix {}".format(self.wf_path, " --fix ".join(self.could_fix))
+            console.print(
+                f"\nTip: Some of these linting errors can automatically be resolved with the following command:\n\n[blue]    {fix_cmd}\n"
+            )
+        if len(self.fix):
+            console.print(
+                "Automatic fixes applied. Please check with 'git diff' and revert any changes you do not want with 'git checkout <file>'."
+            )
+
+    def _print_summary(self):
+        console = Console(force_terminal=nf_core.utils.rich_force_colors())
+
+        def _s(some_list):
+            if len(some_list) != 1:
+                return "s"
+            return ""
+
         # Summary table
         summary_colour = "red" if len(self.failed) > 0 else "green"
         table = Table(box=rich.box.ROUNDED, style=summary_colour)
@@ -352,16 +391,6 @@ def _s(some_list):
         table.add_row(r"[red][✗] {:>3} Test{} Failed".format(len(self.failed), _s(self.failed)))
         console.print(table)
 
-        if len(self.could_fix):
-            fix_cmd = "nf-core lint {} --fix {}".format(self.wf_path, " --fix ".join(self.could_fix))
-            console.print(
-                f"\nTip: Some of these linting errors can automatically be resolved with the following command:\n\n[blue]    {fix_cmd}\n"
-            )
-        if len(self.fix):
-            console.print(
-                "Automatic fixes applied. Please check with 'git diff' and revert any changes you do not want with 'git checkout <file>'."
-            )
-
     def _get_results_md(self):
         """
         Create a markdown file suitable for posting in a GitHub comment.
diff --git a/nf_core/lint_utils.py b/nf_core/lint_utils.py
new file mode 100644
index 0000000000..b7d39f7587
--- /dev/null
+++ b/nf_core/lint_utils.py
@@ -0,0 +1,32 @@
+import rich
+from rich.console import Console
+from rich.table import Table
+import logging
+
+import nf_core.utils
+
+log = logging.getLogger(__name__)
+
+
+def print_joint_summary(lint_obj, module_lint_obj):
+    """Print a joint summary of the general pipe lint tests and the module lint tests"""
+    nbr_passed = len(lint_obj.passed) + len(module_lint_obj.passed)
+    nbr_ignored = len(lint_obj.ignored)
+    nbr_fixed = len(lint_obj.fixed)
+    nbr_warned = len(lint_obj.warned) + len(module_lint_obj.warned)
+    nbr_failed = len(lint_obj.failed) + len(module_lint_obj.failed)
+
+    def _s(some_length):
+        return "" if some_length == 1 else "s"
+
+    console = Console(force_terminal=nf_core.utils.rich_force_colors())
+    summary_colour = "red" if nbr_failed > 0 else "green"
+    table = Table(box=rich.box.ROUNDED, style=summary_colour)
+    table.add_column(f"LINT RESULTS SUMMARY".format(nbr_passed), no_wrap=True)
+    table.add_row(r"[green][✔] {:>3} Test{} Passed".format(nbr_passed, _s(nbr_passed)))
+    if nbr_fixed:
+        table.add_row(r"[bright blue][?] {:>3} Test{} Fixed".format(nbr_fixed, _s(nbr_fixed)))
+    table.add_row(r"[grey58][?] {:>3} Test{} Ignored".format(nbr_ignored, _s(nbr_ignored)))
+    table.add_row(r"[yellow][!] {:>3} Test Warning{}".format(nbr_warned, _s(nbr_warned)))
+    table.add_row(r"[red][✗] {:>3} Test{} Failed".format(nbr_failed, _s(nbr_failed)))
+    console.print(table)
diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py
index fbc91c469c..6bcb33c970 100644
--- a/nf_core/modules/lint/__init__.py
+++ b/nf_core/modules/lint/__init__.py
@@ -21,6 +21,7 @@
 from rich.console import Console
 from rich.table import Table
 from rich.markdown import Markdown
+from rich.panel import Panel
 import rich
 from nf_core.utils import rich_force_colors
 from nf_core.lint.pipeline_todos import pipeline_todos
@@ -66,7 +67,7 @@ class ModuleLint(ModuleCommand):
     from .module_todos import module_todos
     from .module_version import module_version
 
-    def __init__(self, dir, key=()):
+    def __init__(self, dir):
         self.dir = dir
         try:
             self.repo_type = nf_core.modules.module_utils.get_repo_type(self.dir)
@@ -82,7 +83,6 @@ def __init__(self, dir, key=()):
         # Get lists of modules install in directory
         self.all_local_modules, self.all_nfcore_modules = self.get_installed_modules()
 
-        self.key = key
         self.lint_config = None
         self.modules_json = None
 
@@ -94,7 +94,7 @@ def __init__(self, dir, key=()):
             # Add as first test to load git_sha before module_changes
             self.lint_tests.insert(0, "module_version")
 
-    def lint(self, module=None, all_modules=False, print_results=True, show_passed=False, local=False):
+    def lint(self, module=None, key=(), all_modules=False, print_results=True, show_passed=False, local=False):
         """
         Lint all or one specific module
 
@@ -157,9 +157,9 @@ def lint(self, module=None, all_modules=False, print_results=True, show_passed=F
             log.info(f"Linting module: [magenta]{module}")
 
         # Filter the tests by the key if one is supplied
-        if self.key:
+        if key:
             self.filter_tests_by_key()
-            log.info("Only running tests: '{}'".format("', '".join(self.key)))
+            log.info("Only running tests: '{}'".format("', '".join(key)))
 
         # If it is a pipeline, load the lint config file and the modules.json file
         if self.repo_type == "pipeline":
@@ -187,10 +187,10 @@ def set_up_pipeline_files(self):
                     log.info(f"Ignoring lint test: {test_name}")
                     self.lint_tests.remove(test_name)
 
-    def filter_tests_by_key(self):
+    def filter_tests_by_key(self, key):
         """Filters the tests by the supplied key"""
         # Check that supplied test keys exist
-        bad_keys = [k for k in self.key if k not in self.lint_tests]
+        bad_keys = [k for k in key if k not in self.lint_tests]
         if len(bad_keys) > 0:
             raise AssertionError(
                 "Test name{} not recognised: '{}'".format(
@@ -200,7 +200,7 @@ def filter_tests_by_key(self):
             )
 
         # If -k supplied, only run these tests
-        self.lint_tests = [k for k in self.lint_tests if k in self.key]
+        self.lint_tests = [k for k in self.lint_tests if k in key]
 
     def get_installed_modules(self):
         """
@@ -381,6 +381,9 @@ def _s(some_list):
                 return "s"
             return ""
 
+        # Print module linting results header
+        console.print(Panel("[magenta]General lint results"))
+
         # Table of passed tests
         if len(self.passed) > 0 and show_passed:
             console.print(
@@ -419,6 +422,15 @@ def _s(some_list):
             table = format_result(self.failed, table)
             console.print(table)
 
+    def print_summary(self):
+
+        console = Console(force_terminal=rich_force_colors())
+
+        def _s(some_list):
+            if len(some_list) > 1:
+                return "s"
+            return ""
+
         # Summary table
         table = Table(box=rich.box.ROUNDED)
         table.add_column("[bold green]LINT RESULTS SUMMARY".format(len(self.passed)), no_wrap=True)

From 70d1b1eeffa4cf9da95267dbb6d8480c79facadb Mon Sep 17 00:00:00 2001
From: Erik Danielsson <danielsson.erik.0@gmail.com>
Date: Tue, 6 Jul 2021 16:31:25 +0200
Subject: [PATCH 05/11] Moved message about fix option last in lint output

---
 nf_core/lint/__init__.py         | 21 ++++++---------------
 nf_core/lint_utils.py            | 18 +++++++++++++++++-
 nf_core/modules/lint/__init__.py |  7 ++-----
 3 files changed, 25 insertions(+), 21 deletions(-)

diff --git a/nf_core/lint/__init__.py b/nf_core/lint/__init__.py
index 69eac9e6e0..c2517c5e48 100644
--- a/nf_core/lint/__init__.py
+++ b/nf_core/lint/__init__.py
@@ -5,7 +5,6 @@
 the nf-core community guidelines.
 """
 
-from rich.console import Console
 from rich.markdown import Markdown
 from rich.table import Table
 from rich.panel import Panel
@@ -21,6 +20,7 @@
 
 import nf_core.utils
 import nf_core.lint_utils
+from nf_core.lint_utils import console
 from nf_core.modules.lint import ModuleLint
 
 log = logging.getLogger(__name__)
@@ -55,9 +55,12 @@ def run_linting(
     module_lint_obj = ModuleLint(pipeline_dir)
 
     # Run only the tests we want
-    module_lint_tests = ("module_changes",)
+    module_lint_tests = ("module_changes", "module_version")
     module_lint_obj.filter_tests_by_key(module_lint_tests)
 
+    # Set up files for modules linting test
+    module_lint_obj.set_up_pipeline_files()
+
     # Run the pipeline linting tests
     try:
         lint_obj._lint_pipeline()
@@ -76,6 +79,7 @@ def run_linting(
     lint_obj._print_results(show_passed)
     module_lint_obj._print_results(show_passed)
     nf_core.lint_utils.print_joint_summary(lint_obj, module_lint_obj)
+    nf_core.lint_utils.print_fixes(lint_obj, module_lint_obj)
 
     # Save results to Markdown file
     if md_fn is not None:
@@ -306,7 +310,6 @@ def _print_results(self, show_passed):
         """
 
         log.debug("Printing final results")
-        console = Console(force_terminal=nf_core.utils.rich_force_colors())
 
         # Helper function to format test links nicely
         def format_result(test_results, table):
@@ -361,19 +364,7 @@ def _s(some_list):
             table = format_result(self.failed, table)
             console.print(table)
 
-        if len(self.could_fix):
-            fix_cmd = "nf-core lint {} --fix {}".format(self.wf_path, " --fix ".join(self.could_fix))
-            console.print(
-                f"\nTip: Some of these linting errors can automatically be resolved with the following command:\n\n[blue]    {fix_cmd}\n"
-            )
-        if len(self.fix):
-            console.print(
-                "Automatic fixes applied. Please check with 'git diff' and revert any changes you do not want with 'git checkout <file>'."
-            )
-
     def _print_summary(self):
-        console = Console(force_terminal=nf_core.utils.rich_force_colors())
-
         def _s(some_list):
             if len(some_list) != 1:
                 return "s"
diff --git a/nf_core/lint_utils.py b/nf_core/lint_utils.py
index b7d39f7587..6e2084922e 100644
--- a/nf_core/lint_utils.py
+++ b/nf_core/lint_utils.py
@@ -7,6 +7,9 @@
 
 log = logging.getLogger(__name__)
 
+# Create a console used by all lint tests
+console = Console(force_terminal=nf_core.utils.rich_force_colors())
+
 
 def print_joint_summary(lint_obj, module_lint_obj):
     """Print a joint summary of the general pipe lint tests and the module lint tests"""
@@ -19,7 +22,6 @@ def print_joint_summary(lint_obj, module_lint_obj):
     def _s(some_length):
         return "" if some_length == 1 else "s"
 
-    console = Console(force_terminal=nf_core.utils.rich_force_colors())
     summary_colour = "red" if nbr_failed > 0 else "green"
     table = Table(box=rich.box.ROUNDED, style=summary_colour)
     table.add_column(f"LINT RESULTS SUMMARY".format(nbr_passed), no_wrap=True)
@@ -30,3 +32,17 @@ def _s(some_length):
     table.add_row(r"[yellow][!] {:>3} Test Warning{}".format(nbr_warned, _s(nbr_warned)))
     table.add_row(r"[red][✗] {:>3} Test{} Failed".format(nbr_failed, _s(nbr_failed)))
     console.print(table)
+
+
+def print_fixes(lint_obj, module_lint_obj):
+    """Prints available and applied fixes"""
+
+    if len(lint_obj.could_fix):
+        fix_cmd = "nf-core lint {} --fix {}".format(lint_obj.wf_path, " --fix ".join(lint_obj.could_fix))
+        console.print(
+            f"\nTip: Some of these linting errors can automatically be resolved with the following command:\n\n[blue]    {fix_cmd}\n"
+        )
+    if len(lint_obj.fix):
+        console.print(
+            "Automatic fixes applied. Please check with 'git diff' and revert any changes you do not want with 'git checkout <file>'."
+        )
diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py
index 6bcb33c970..c84f181948 100644
--- a/nf_core/modules/lint/__init__.py
+++ b/nf_core/modules/lint/__init__.py
@@ -18,7 +18,6 @@
 import rich
 import yaml
 import json
-from rich.console import Console
 from rich.table import Table
 from rich.markdown import Markdown
 from rich.panel import Panel
@@ -29,8 +28,10 @@
 
 import nf_core.utils
 import nf_core.modules.module_utils
+
 from nf_core.modules.modules_repo import ModulesRepo
 from nf_core.modules.nfcore_module import NFCoreModule
+from nf_core.lint_utils import console
 
 log = logging.getLogger(__name__)
 
@@ -335,7 +336,6 @@ def _print_results(self, show_passed=False):
         """
 
         log.debug("Printing final results")
-        console = Console(force_terminal=rich_force_colors())
 
         # Sort the results
         self.passed.sort(key=operator.attrgetter("message", "module_name"))
@@ -423,9 +423,6 @@ def _s(some_list):
             console.print(table)
 
     def print_summary(self):
-
-        console = Console(force_terminal=rich_force_colors())
-
         def _s(some_list):
             if len(some_list) > 1:
                 return "s"

From 842a6c329f8c267c1bbec1ac651e6df364194cac Mon Sep 17 00:00:00 2001
From: Erik Danielsson <danielsson.erik.0@gmail.com>
Date: Tue, 6 Jul 2021 16:50:33 +0200
Subject: [PATCH 06/11] small fixes

---
 nf_core/lint/__init__.py         | 4 ++--
 nf_core/modules/lint/__init__.py | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/nf_core/lint/__init__.py b/nf_core/lint/__init__.py
index c2517c5e48..d0b61be7c7 100644
--- a/nf_core/lint/__init__.py
+++ b/nf_core/lint/__init__.py
@@ -43,7 +43,7 @@ def run_linting(
     """
 
     # Create the lint object
-    lint_obj = PipelineLint(pipeline_dir, release_mode, fix, key, fail_ignored, show_passed)
+    lint_obj = PipelineLint(pipeline_dir, release_mode, fix, key, fail_ignored)
 
     # Load the various pipeline configs
     lint_obj._load_lint_config()
@@ -139,7 +139,7 @@ class PipelineLint(nf_core.utils.Pipeline):
     from .template_strings import template_strings
     from .version_consistency import version_consistency
 
-    def __init__(self, wf_path, release_mode=False, fix=(), key=(), fail_ignored=False, show_passed=False):
+    def __init__(self, wf_path, release_mode=False, fix=(), key=(), fail_ignored=False):
         """Initialise linting object"""
 
         # Initialise the parent object
diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py
index c84f181948..d3e6cd5daf 100644
--- a/nf_core/modules/lint/__init__.py
+++ b/nf_core/modules/lint/__init__.py
@@ -382,7 +382,7 @@ def _s(some_list):
             return ""
 
         # Print module linting results header
-        console.print(Panel("[magenta]General lint results"))
+        console.print(Panel("[magenta]Module lint results"))
 
         # Table of passed tests
         if len(self.passed) > 0 and show_passed:

From 348856b27c17b2eecb41034b09265d0b0dcd053b Mon Sep 17 00:00:00 2001
From: Erik Danielsson <danielsson.erik.0@gmail.com>
Date: Fri, 9 Jul 2021 11:00:41 +0200
Subject: [PATCH 07/11] Apply changes from code review

---
 nf_core/modules/lint/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py
index 15a39ab890..4b097d9207 100644
--- a/nf_core/modules/lint/__init__.py
+++ b/nf_core/modules/lint/__init__.py
@@ -159,7 +159,7 @@ def lint(self, module=None, key=(), all_modules=False, print_results=True, show_
 
         # Filter the tests by the key if one is supplied
         if key:
-            self.filter_tests_by_key()
+            self.filter_tests_by_key(key)
             log.info("Only running tests: '{}'".format("', '".join(key)))
 
         # If it is a pipeline, load the lint config file and the modules.json file

From f3bf644a4df1e2aa2105ce0d5e66f9f7fd9d3869 Mon Sep 17 00:00:00 2001
From: Erik Danielsson <53212377+ErikDanielsson@users.noreply.github.com>
Date: Fri, 9 Jul 2021 11:01:12 +0200
Subject: [PATCH 08/11] Update nf_core/modules/lint/__init__.py

Co-authored-by: Kevin Menden <kevin.menden@live.com>
---
 nf_core/modules/lint/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py
index 4b097d9207..246c6c80da 100644
--- a/nf_core/modules/lint/__init__.py
+++ b/nf_core/modules/lint/__init__.py
@@ -300,7 +300,7 @@ def lint_module(self, mod, local=False):
         Perform linting on one module
 
         If the module is a local module we only check the `main.nf` file,
-        and it issue warnings instead of failures.
+        and issue warnings instead of failures.
 
         If the module is a nf-core module we check for existence of the files
         - main.nf

From ffcb0556dface07cdf3da99c7ef8b5f45a4fad5b Mon Sep 17 00:00:00 2001
From: Erik Danielsson <danielsson.erik.0@gmail.com>
Date: Fri, 9 Jul 2021 11:10:37 +0200
Subject: [PATCH 09/11] Fix errors with 'key'

---
 nf_core/__main__.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index 2855b04afe..425ce9a45b 100755
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -543,9 +543,9 @@ def lint(ctx, tool, dir, key, all, local, passed):
     nf-core/modules repository.
     """
     try:
-        module_lint = nf_core.modules.ModuleLint(dir=dir, key=key)
+        module_lint = nf_core.modules.ModuleLint(dir=dir)
         module_lint.modules_repo = ctx.obj["modules_repo_obj"]
-        module_lint.lint(module=tool, all_modules=all, print_results=True, local=local, show_passed=passed)
+        module_lint.lint(module=tool, key=key, all_modules=all, print_results=True, local=local, show_passed=passed)
         if len(module_lint.failed) > 0:
             sys.exit(1)
     except nf_core.modules.lint.ModuleLintException as e:

From 87d85a1258ef04860a2cb76a181afd0ffa1f1b5e Mon Sep 17 00:00:00 2001
From: Erik Danielsson <danielsson.erik.0@gmail.com>
Date: Fri, 9 Jul 2021 11:19:16 +0200
Subject: [PATCH 10/11] Print lint summary in modules lint

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

diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py
index 246c6c80da..af5ed69722 100644
--- a/nf_core/modules/lint/__init__.py
+++ b/nf_core/modules/lint/__init__.py
@@ -422,6 +422,9 @@ def _s(some_list):
             table = format_result(self.failed, table)
             console.print(table)
 
+        # Print lint summary
+        self.print_summary()
+
     def print_summary(self):
         def _s(some_list):
             if len(some_list) > 1:

From 0060db2e3d41aeabb1338d450b61cfc8226bce63 Mon Sep 17 00:00:00 2001
From: Erik Danielsson <danielsson.erik.0@gmail.com>
Date: Fri, 9 Jul 2021 11:23:46 +0200
Subject: [PATCH 11/11] Fix summary output

---
 nf_core/modules/lint/__init__.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py
index af5ed69722..c870d136d3 100644
--- a/nf_core/modules/lint/__init__.py
+++ b/nf_core/modules/lint/__init__.py
@@ -176,6 +176,7 @@ def lint(self, module=None, key=(), all_modules=False, print_results=True, show_
 
         if print_results:
             self._print_results(show_passed=show_passed)
+            self.print_summary()
 
     def set_up_pipeline_files(self):
         self.load_lint_config()
@@ -422,9 +423,6 @@ def _s(some_list):
             table = format_result(self.failed, table)
             console.print(table)
 
-        # Print lint summary
-        self.print_summary()
-
     def print_summary(self):
         def _s(some_list):
             if len(some_list) > 1: