From a754fe0845f0e28ae0398625d8132a6047aa991e Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 14 Aug 2024 15:07:38 +0200
Subject: [PATCH 01/63] add schema checking for draft 2020-12

---
 nf_core/pipelines/lint/schema_lint.py | 32 ++++++++++++++++++++++-----
 nf_core/pipelines/schema.py           | 21 +++++++++++++-----
 requirements.txt                      |  2 +-
 3 files changed, 44 insertions(+), 11 deletions(-)

diff --git a/nf_core/pipelines/lint/schema_lint.py b/nf_core/pipelines/lint/schema_lint.py
index 6786c5012d..4007bf8fe5 100644
--- a/nf_core/pipelines/lint/schema_lint.py
+++ b/nf_core/pipelines/lint/schema_lint.py
@@ -16,26 +16,26 @@ def schema_lint(self):
     The lint test checks the schema for the following:
 
     * Schema should be a valid JSON file
-    * Schema should adhere to `JSONSchema <https://json-schema.org/>`_, Draft 7.
+    * Schema should adhere to `JSONSchema <https://json-schema.org/>`_, Draft 7 or Draft 2020-12.
     * Parameters can be described in two places:
 
         * As ``properties`` in the top-level schema object
-        * As ``properties`` within subschemas listed in a top-level ``definitions`` objects
+        * As ``properties`` within subschemas listed in a top-level ``definitions``(draft 7) or ``$defs``(draft 2020-12) objects
 
     * The schema must describe at least one parameter
     * There must be no duplicate parameter IDs across the schema and definition subschema
-    * All subschema in ``definitions`` must be referenced in the top-level ``allOf`` key
+    * All subschema in ``definitions`` or ``$defs`` must be referenced in the top-level ``allOf`` key
     * The top-level ``allOf`` key must not describe any non-existent definitions
     * Default parameters in the schema must be valid
     * Core top-level schema attributes should exist and be set as follows:
 
-        * ``$schema``: ``https://json-schema.org/draft-07/schema``
+        * ``$schema``: ``https://json-schema.org/draft-07/schema`` or ``https://json-schema.org/draft/2020-12/schema``
         * ``$id``: URL to the raw schema file, eg. ``https://raw.githubusercontent.com/YOURPIPELINE/master/nextflow_schema.json``
         * ``title``: ``YOURPIPELINE pipeline parameters``
         * ``description``: The pipeline config ``manifest.description``
     * That the ``input`` property is defined and has a mimetype. A list of common mimetypes can be found `here <https://developer.mozilla.org/en-US/docs/Web/HTTP/Basics_of_HTTP/MIME_types/Common_types>`_.
 
-    For example, an *extremely* minimal schema could look like this:
+    For example, an *extremely* minimal schema could look like this (draft 7):
 
     .. code-block:: json
 
@@ -57,6 +57,28 @@ def schema_lint(self):
          "allOf": [{"$ref": "#/definitions/my_first_group"}]
        }
 
+    Or this (draft 2020-12):
+
+    .. code-block:: json
+
+       {
+         "$schema": "https://json-schema.org/draft/2020-12/schema",
+         "$id": "https://raw.githubusercontent.com/YOURPIPELINE/master/nextflow_schema.json",
+         "title": "YOURPIPELINE pipeline parameters",
+         "description": "This pipeline is for testing",
+         "properties": {
+           "first_param": { "type": "string" }
+         },
+         "$defs": {
+           "my_first_group": {
+             "properties": {
+               "second_param": { "type": "string" }
+             }
+           }
+         },
+         "allOf": [{"$ref": "#/$defs/my_first_group"}]
+       }
+
     .. tip:: You can check your pipeline schema without having to run the entire pipeline lint
              by running ``nf-core pipelines schema lint`` instead of ``nf-core pipelines lint``
     """
diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index 7f562bff38..854bddccc0 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -359,11 +359,22 @@ def validate_schema(self, schema=None):
         """
         if schema is None:
             schema = self.schema
-        try:
-            jsonschema.Draft7Validator.check_schema(schema)
-            log.debug("JSON Schema Draft7 validated")
-        except jsonschema.exceptions.SchemaError as e:
-            raise AssertionError(f"Schema does not validate as Draft 7 JSON Schema:\n {e}")
+
+        schema_draft = schema["$schema"]
+        if schema_draft == "https://json-schema.org/draft-07/schema":
+            try:
+                jsonschema.Draft7Validator.check_schema(schema)
+                log.debug("JSON Schema Draft7 validated")
+            except jsonschema.exceptions.SchemaError as e:
+                raise AssertionError(f"Schema does not validate as Draft 7 JSON Schema:\n {e}")
+        elif schema_draft == "https://json-schema.org/draft/2020-12/schema":
+            try:
+                jsonschema.Draft202012Validator.check_schema(schema)
+                log.debug("JSON Schema Draft2020-12 validated")
+            except jsonschema.exceptions.SchemaError as e:
+                raise AssertionError(f"Schema does not validate as Draft 2020-12 JSON Schema:\n {e}")
+        else:
+            raise AssertionError(f"Unsupported JSON schema draft detected: ${schema_draft}. Use draft 7 or 2020-12 instead.")
 
         param_keys = list(schema.get("properties", {}).keys())
         num_params = len(param_keys)
diff --git a/requirements.txt b/requirements.txt
index fb658be2fb..eba6460f03 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -3,7 +3,7 @@ filetype
 GitPython
 PyGithub
 jinja2
-jsonschema>=3.0
+jsonschema>=4.0
 markdown>=3.3
 packaging
 pillow

From 464f16e982337699382e66e3b1da21af4f01dd7a Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 14 Aug 2024 15:26:52 +0200
Subject: [PATCH 02/63] update validate schema

---
 nf_core/pipelines/schema.py | 31 +++++++++++++++++++++++--------
 1 file changed, 23 insertions(+), 8 deletions(-)

diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index 854bddccc0..abdad719f6 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -378,17 +378,32 @@ def validate_schema(self, schema=None):
 
         param_keys = list(schema.get("properties", {}).keys())
         num_params = len(param_keys)
-        for d_key, d_schema in schema.get("definitions", {}).items():
+        schema_defs = dict()
+        defs_notation = ""
+        if "$defs" in schema:
+            schema_defs = schema.get("$defs", {}).items()
+            defs_notation = "$defs"
+        elif "definitions" in schema:
+            schema_defs = schema.get("definitions", {}).items()
+            defs_notation = "definitions"
+        elif "defs" in schema:
+            # nf-schema v2.0.0 only supported defs. this has been changed to $defs in nf-schema v2.1.0
+            # this line prevents the breakage of schemas created for v2.0.0
+            schema_defs = schema.get("defs", {}).items()
+            defs_notation = "defs"
+
+        for d_key, d_schema in schema_defs:
             # Check that this definition is mentioned in allOf
             if "allOf" not in schema:
                 raise AssertionError("Schema has definitions, but no allOf key")
             in_allOf = False
             for allOf in schema.get("allOf", []):
-                if allOf["$ref"] == f"#/definitions/{d_key}":
+                if allOf["$ref"] == f"#/{defs_notation}/{d_key}":
                     in_allOf = True
             if not in_allOf:
-                raise AssertionError(f"Definition subschema `{d_key}` not included in schema `allOf`")
+                raise AssertionError(f"Definition subschema `#{defs_notation}/{d_key}` not included in schema `allOf`")
 
+            # TODO add support for nested parameters
             for d_param_id in d_schema.get("properties", {}):
                 # Check that we don't have any duplicate parameter IDs in different definitions
                 if d_param_id in param_keys:
@@ -398,11 +413,11 @@ def validate_schema(self, schema=None):
 
         # Check that everything in allOf exists
         for allOf in schema.get("allOf", []):
-            if "definitions" not in schema:
-                raise AssertionError("Schema has allOf, but no definitions")
-            def_key = allOf["$ref"][14:]
-            if def_key not in schema.get("definitions", {}):
-                raise AssertionError(f"Subschema `{def_key}` found in `allOf` but not `definitions`")
+            _, allOf_defs_notation, def_key = allOf["$ref"].split("/") # "#/<defs_notation>/<def_name>"
+            if allOf_defs_notation not in schema:
+                raise AssertionError(f"Schema has allOf, but no {allOf_defs_notation}")
+            if def_key not in schema.get(allOf_defs_notation, {}):
+                raise AssertionError(f"Subschema `{def_key}` found in `allOf` but not `{allOf_defs_notation}`")
 
         # Check that the schema describes at least one parameter
         if num_params == 0:

From 6658449cc892021782a22885c3db63c0215254b6 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 14 Aug 2024 15:51:27 +0200
Subject: [PATCH 03/63] update more code to support draft 2020-12

---
 nf_core/pipelines/schema.py | 55 ++++++++++++++++++++-----------------
 1 file changed, 30 insertions(+), 25 deletions(-)

diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index abdad719f6..398783d5a8 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -116,8 +116,26 @@ def load_schema(self):
             self.schema = json.load(fh)
         self.schema_defaults = {}
         self.schema_params = {}
+        if "$schema" not in self.schema:
+            raise AssertionError("Schema missing top-level `$schema` attribute")        
+        self.schema_draft = self.schema["$schema"]
+        self.defs_notation = self.get_defs_notation()
         log.debug(f"JSON file loaded: {self.schema_filename}")
 
+    def get_defs_notation(self, schema=None):
+        if schema is None:
+            schema = self.schema
+
+        if "$defs" in schema:
+            defs_notation = "$defs"
+        elif "definitions" in schema:
+            defs_notation = "definitions"
+        elif "defs" in schema:
+            # nf-schema v2.0.0 only supported defs. this has been changed to $defs in nf-schema v2.1.0
+            # this line prevents the breakage of schemas created for v2.0.0
+            defs_notation = "defs"
+        return defs_notation
+
     def sanitise_param_default(self, param):
         """
         Given a param, ensure that the default value is the correct variable type
@@ -168,10 +186,11 @@ def get_schema_defaults(self) -> None:
                 if param["default"] is not None:
                     self.schema_defaults[p_key] = param["default"]
 
+        # TODO add support for nested parameters
         # Grouped schema properties in subschema definitions
-        for defn_name, definition in self.schema.get("definitions", {}).items():
+        for defn_name, definition in self.schema.get(self.defs_notation, {}).items():
             for p_key, param in definition.get("properties", {}).items():
-                self.schema_params[p_key] = ("definitions", defn_name, "properties", p_key)
+                self.schema_params[p_key] = (self.defs_notation, defn_name, "properties", p_key)
                 if "default" in param:
                     param = self.sanitise_param_default(param)
                     if param["default"] is not None:
@@ -248,13 +267,14 @@ def validate_default_params(self):
         if self.schema is None:
             log.error("[red][✗] Pipeline schema not found")
         try:
+            # TODO add support for nested parameters
             # Make copy of schema and remove required flags
             schema_no_required = copy.deepcopy(self.schema)
             if "required" in schema_no_required:
                 schema_no_required.pop("required")
-            for group_key, group in schema_no_required.get("definitions", {}).items():
+            for group_key, group in schema_no_required.get(self.defs_notation, {}).items():
                 if "required" in group:
-                    schema_no_required["definitions"][group_key].pop("required")
+                    schema_no_required[self.defs_notation][group_key].pop("required")
             jsonschema.validate(self.schema_defaults, schema_no_required)
         except jsonschema.exceptions.ValidationError as e:
             raise AssertionError(f"Default parameters are invalid: {e.message}")
@@ -360,6 +380,8 @@ def validate_schema(self, schema=None):
         if schema is None:
             schema = self.schema
 
+        if "$schema" not in schema:
+            raise AssertionError("Schema missing top-level `$schema` attribute")
         schema_draft = schema["$schema"]
         if schema_draft == "https://json-schema.org/draft-07/schema":
             try:
@@ -374,25 +396,14 @@ def validate_schema(self, schema=None):
             except jsonschema.exceptions.SchemaError as e:
                 raise AssertionError(f"Schema does not validate as Draft 2020-12 JSON Schema:\n {e}")
         else:
-            raise AssertionError(f"Unsupported JSON schema draft detected: ${schema_draft}. Use draft 7 or 2020-12 instead.")
+            raise AssertionError(f"Schema `$schema` should be `https://json-schema.org/draft/2020-12/schema` or `https://json-schema.org/draft-07/schema` \n Found `{schema_draft}`")
 
         param_keys = list(schema.get("properties", {}).keys())
         num_params = len(param_keys)
         schema_defs = dict()
-        defs_notation = ""
-        if "$defs" in schema:
-            schema_defs = schema.get("$defs", {}).items()
-            defs_notation = "$defs"
-        elif "definitions" in schema:
-            schema_defs = schema.get("definitions", {}).items()
-            defs_notation = "definitions"
-        elif "defs" in schema:
-            # nf-schema v2.0.0 only supported defs. this has been changed to $defs in nf-schema v2.1.0
-            # this line prevents the breakage of schemas created for v2.0.0
-            schema_defs = schema.get("defs", {}).items()
-            defs_notation = "defs"
+        defs_notation = self.get_defs_notation(schema)
 
-        for d_key, d_schema in schema_defs:
+        for d_key, d_schema in schema.get(defs_notation, {}).items():
             # Check that this definition is mentioned in allOf
             if "allOf" not in schema:
                 raise AssertionError("Schema has definitions, but no allOf key")
@@ -428,7 +439,7 @@ def validate_schema(self, schema=None):
     def validate_schema_title_description(self, schema=None):
         """
         Extra validation command for linting.
-        Checks that the schema "$id", "title" and "description" attributes match the piipeline config.
+        Checks that the schema "$id", "title" and "description" attributes match the pipeline config.
         """
         if schema is None:
             schema = self.schema
@@ -436,12 +447,6 @@ def validate_schema_title_description(self, schema=None):
             log.debug("Pipeline schema not set - skipping validation of top-level attributes")
             return None
 
-        if "$schema" not in self.schema:
-            raise AssertionError("Schema missing top-level `$schema` attribute")
-        schema_attr = "http://json-schema.org/draft-07/schema"
-        if self.schema["$schema"] != schema_attr:
-            raise AssertionError(f"Schema `$schema` should be `{schema_attr}`\n Found `{self.schema['$schema']}`")
-
         if self.pipeline_manifest == {}:
             self.get_wf_params()
 

From 6ecde202d05baa2944f582f0b0835ea73765006b Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 14 Aug 2024 16:11:47 +0200
Subject: [PATCH 04/63] fix draft 7 schema using http

---
 nf_core/pipelines/schema.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index 398783d5a8..e1931b9007 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -383,7 +383,7 @@ def validate_schema(self, schema=None):
         if "$schema" not in schema:
             raise AssertionError("Schema missing top-level `$schema` attribute")
         schema_draft = schema["$schema"]
-        if schema_draft == "https://json-schema.org/draft-07/schema":
+        if schema_draft == "https://json-schema.org/draft-07/schema" or schema_draft == "http://json-schema.org/draft-07/schema":
             try:
                 jsonschema.Draft7Validator.check_schema(schema)
                 log.debug("JSON Schema Draft7 validated")

From 36fad24c7eda672fce4a885fe2e7d5610b022a9c Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 14 Aug 2024 16:18:08 +0200
Subject: [PATCH 05/63] ruff

---
 nf_core/pipelines/schema.py | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index e1931b9007..188861fff1 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -400,7 +400,6 @@ def validate_schema(self, schema=None):
 
         param_keys = list(schema.get("properties", {}).keys())
         num_params = len(param_keys)
-        schema_defs = dict()
         defs_notation = self.get_defs_notation(schema)
 
         for d_key, d_schema in schema.get(defs_notation, {}).items():
@@ -424,11 +423,11 @@ def validate_schema(self, schema=None):
 
         # Check that everything in allOf exists
         for allOf in schema.get("allOf", []):
-            _, allOf_defs_notation, def_key = allOf["$ref"].split("/") # "#/<defs_notation>/<def_name>"
-            if allOf_defs_notation not in schema:
-                raise AssertionError(f"Schema has allOf, but no {allOf_defs_notation}")
-            if def_key not in schema.get(allOf_defs_notation, {}):
-                raise AssertionError(f"Subschema `{def_key}` found in `allOf` but not `{allOf_defs_notation}`")
+            _, allof_defs_notation, def_key = allOf["$ref"].split("/") # "#/<defs_notation>/<def_name>"
+            if allof_defs_notation not in schema:
+                raise AssertionError(f"Schema has allOf, but no {allof_defs_notation}")
+            if def_key not in schema.get(allof_defs_notation, {}):
+                raise AssertionError(f"Subschema `{def_key}` found in `allOf` but not `{allof_defs_notation}`")
 
         # Check that the schema describes at least one parameter
         if num_params == 0:

From 6777694b20726f333dd8eae416917c3324c3e158 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 14 Aug 2024 16:33:00 +0200
Subject: [PATCH 06/63] fix tests + add draft 2020-12 as default draft

---
 nf_core/pipelines/schema.py    | 2 ++
 tests/pipelines/test_schema.py | 5 ++++-
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index 188861fff1..1555a4198d 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -46,6 +46,8 @@ def __init__(self):
         self.web_schema_build_url = "https://nf-co.re/pipeline_schema_builder"
         self.web_schema_build_web_url = None
         self.web_schema_build_api_url = None
+        self.schema_draft = "https://json-schema.org/draft/2020-12/schema"
+        self.defs_notation = "$defs"
 
     def get_schema_path(
         self, path: Union[str, Path], local_only: bool = False, revision: Union[str, None] = None
diff --git a/tests/pipelines/test_schema.py b/tests/pipelines/test_schema.py
index 633de3db69..777d959e66 100644
--- a/tests/pipelines/test_schema.py
+++ b/tests/pipelines/test_schema.py
@@ -175,6 +175,7 @@ def test_validate_schema_fail_duplicate_ids(self):
         Check that the schema validation fails when we have duplicate IDs in definition subschema
         """
         self.schema_obj.schema = {
+            "$schema": "http://json-schema.org/draft-07/schema",
             "definitions": {"groupOne": {"properties": {"foo": {}}}, "groupTwo": {"properties": {"foo": {}}}},
             "allOf": [{"$ref": "#/definitions/groupOne"}, {"$ref": "#/definitions/groupTwo"}],
         }
@@ -187,18 +188,20 @@ def test_validate_schema_fail_missing_def(self):
         Check that the schema validation fails when we a definition in allOf is not in definitions
         """
         self.schema_obj.schema = {
+            "$schema": "http://json-schema.org/draft-07/schema",
             "definitions": {"groupOne": {"properties": {"foo": {}}}, "groupTwo": {"properties": {"bar": {}}}},
             "allOf": [{"$ref": "#/definitions/groupOne"}],
         }
         with pytest.raises(AssertionError) as exc_info:
             self.schema_obj.validate_schema(self.schema_obj.schema)
-        assert exc_info.value.args[0] == "Definition subschema `groupTwo` not included in schema `allOf`"
+        assert exc_info.value.args[0] == "Definition subschema `#/definitions/groupTwo` not included in schema `allOf`"
 
     def test_validate_schema_fail_unexpected_allof(self):
         """
         Check that the schema validation fails when we an unrecognised definition is in allOf
         """
         self.schema_obj.schema = {
+            "$schema": "http://json-schema.org/draft-07/schema",
             "definitions": {"groupOne": {"properties": {"foo": {}}}, "groupTwo": {"properties": {"bar": {}}}},
             "allOf": [
                 {"$ref": "#/definitions/groupOne"},

From 0dfd15ded935054fc8d185b5fd36223505441ff7 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 14 Aug 2024 16:34:01 +0200
Subject: [PATCH 07/63] fix typo

---
 nf_core/pipelines/schema.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index 1555a4198d..ba5af51f96 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -413,7 +413,7 @@ def validate_schema(self, schema=None):
                 if allOf["$ref"] == f"#/{defs_notation}/{d_key}":
                     in_allOf = True
             if not in_allOf:
-                raise AssertionError(f"Definition subschema `#{defs_notation}/{d_key}` not included in schema `allOf`")
+                raise AssertionError(f"Definition subschema `#/{defs_notation}/{d_key}` not included in schema `allOf`")
 
             # TODO add support for nested parameters
             for d_param_id in d_schema.get("properties", {}):

From 7f29f373a82ed1ada16b6b493f10d724a4b879cc Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 14 Aug 2024 16:37:06 +0200
Subject: [PATCH 08/63] ruff

---
 nf_core/pipelines/schema.py | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index ba5af51f96..43058d4e6f 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -119,7 +119,7 @@ def load_schema(self):
         self.schema_defaults = {}
         self.schema_params = {}
         if "$schema" not in self.schema:
-            raise AssertionError("Schema missing top-level `$schema` attribute")        
+            raise AssertionError("Schema missing top-level `$schema` attribute")
         self.schema_draft = self.schema["$schema"]
         self.defs_notation = self.get_defs_notation()
         log.debug(f"JSON file loaded: {self.schema_filename}")
@@ -385,7 +385,10 @@ def validate_schema(self, schema=None):
         if "$schema" not in schema:
             raise AssertionError("Schema missing top-level `$schema` attribute")
         schema_draft = schema["$schema"]
-        if schema_draft == "https://json-schema.org/draft-07/schema" or schema_draft == "http://json-schema.org/draft-07/schema":
+        if (
+            schema_draft == "https://json-schema.org/draft-07/schema"
+            or schema_draft == "http://json-schema.org/draft-07/schema"
+        ):
             try:
                 jsonschema.Draft7Validator.check_schema(schema)
                 log.debug("JSON Schema Draft7 validated")
@@ -398,7 +401,9 @@ def validate_schema(self, schema=None):
             except jsonschema.exceptions.SchemaError as e:
                 raise AssertionError(f"Schema does not validate as Draft 2020-12 JSON Schema:\n {e}")
         else:
-            raise AssertionError(f"Schema `$schema` should be `https://json-schema.org/draft/2020-12/schema` or `https://json-schema.org/draft-07/schema` \n Found `{schema_draft}`")
+            raise AssertionError(
+                f"Schema `$schema` should be `https://json-schema.org/draft/2020-12/schema` or `https://json-schema.org/draft-07/schema` \n Found `{schema_draft}`"
+            )
 
         param_keys = list(schema.get("properties", {}).keys())
         num_params = len(param_keys)
@@ -425,7 +430,7 @@ def validate_schema(self, schema=None):
 
         # Check that everything in allOf exists
         for allOf in schema.get("allOf", []):
-            _, allof_defs_notation, def_key = allOf["$ref"].split("/") # "#/<defs_notation>/<def_name>"
+            _, allof_defs_notation, def_key = allOf["$ref"].split("/")  # "#/<defs_notation>/<def_name>"
             if allof_defs_notation not in schema:
                 raise AssertionError(f"Schema has allOf, but no {allof_defs_notation}")
             if def_key not in schema.get(allof_defs_notation, {}):

From 730c6779779d4e14512df25c043eb02efe6d1659 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 14 Aug 2024 17:34:53 +0200
Subject: [PATCH 09/63] add checks for nf-validation and nf-schema plugin
 config

---
 nf_core/pipelines/lint/nextflow_config.py | 33 +++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py
index 96323af94d..8fe933d102 100644
--- a/nf_core/pipelines/lint/nextflow_config.py
+++ b/nf_core/pipelines/lint/nextflow_config.py
@@ -336,6 +336,7 @@ def nextflow_config(self) -> Dict[str, List[str]]:
             )
 
     # Check for the availability of the "test" configuration profile by parsing nextflow.config
+    # Also check for the presence of nf-validation/nf-schema and check if they have pinned versions
     with open(Path(self.wf_path, "nextflow.config")) as f:
         content = f.read()
 
@@ -363,6 +364,38 @@ def nextflow_config(self) -> Dict[str, List[str]]:
             else:
                 failed.append("nextflow.config does not contain configuration profile `test`")
 
+        match_plugins = re.search(r"\bplugins\s*\{([^}]+)}", cleaned_content, re.MULTILINE)
+        if not match_plugins:
+            failed.append(
+                "nextflow.config does not contain `plugins` scope, but `nf-validation` or `nf-schema` plugins are required"
+            )
+        else:
+            found_plugins = {}
+            for line in match_plugins.group(1).split("\n"):
+                cleaned_line = line.split("//")[0].strip().replace("\"", "'")
+                if "id" not in line: continue
+                match_line = re.search(r"\bid\s'([^']+)'", cleaned_line)
+                if not match_line:
+                    failed.append(f"nextflow.config contains an invalid plugins identifier: {cleaned_line}")
+                    continue
+                plugin = match_line.group(1)
+                name = plugin.split("@")[0]
+                version = ""
+                if "@" in plugin:
+                    version = plugin.split("@")[1]
+                found_plugins[name] = version
+
+            if len(found_plugins) == 0:
+                failed.append("nextflow.config contains an empty plugins scope")
+            elif "nf-validation" in found_plugins and "nf-schema" in found_plugins:
+                failed.append("nextflow.config contains both nf-validation and nf-schema")
+            elif "nf-validation" in found_plugins and found_plugins["nf-validation"] == "":
+                failed.append("nextflow.config contains an unpinned version of nf-validation")
+            elif "nf-schema" in found_plugins and found_plugins["nf-schema"] == "":
+                failed.append("nextflow.config contains an unpinned version of nf-schema")
+            elif "nf-validation" not in found_plugins and "nf-schema" not in found_plugins:
+                failed.append("nextflow.config does not contain `nf-validation` or `nf-schema` in the plugins scope")
+
     # Check that the default values in nextflow.config match the default values defined in the nextflow_schema.json
     ignore_defaults = []
     for item in ignore_configs:

From 7fbbff7a412c64ef67417dd60a722d67f6d37647 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 14 Aug 2024 17:39:10 +0200
Subject: [PATCH 10/63] linting fully works now!

---
 nf_core/pipelines/lint/schema_description.py | 5 +++--
 nf_core/pipelines/schema.py                  | 2 +-
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/nf_core/pipelines/lint/schema_description.py b/nf_core/pipelines/lint/schema_description.py
index d617e40949..b586cc5242 100644
--- a/nf_core/pipelines/lint/schema_description.py
+++ b/nf_core/pipelines/lint/schema_description.py
@@ -36,8 +36,9 @@ def schema_description(self):
                 warned.append(f"Ungrouped param in schema: `{up}`")
 
     # Iterate over groups and add warning for parameters without a description
-    for group_key in self.schema_obj.schema["definitions"].keys():
-        group = self.schema_obj.schema["definitions"][group_key]
+    defs_notation = self.schema_obj.defs_notation
+    for group_key in self.schema_obj.schema[defs_notation].keys():
+        group = self.schema_obj.schema[defs_notation][group_key]
         for param_key, param in group["properties"].items():
             if param_key in ignore_params:
                 ignored.append(f"Ignoring description check for param in schema: `{param_key}`")
diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index 43058d4e6f..c70332beb2 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -203,7 +203,7 @@ def get_schema_types(self) -> None:
         for name, param in self.schema.get("properties", {}).items():
             if "type" in param:
                 self.schema_types[name] = param["type"]
-        for _, definition in self.schema.get("definitions", {}).items():
+        for _, definition in self.schema.get(self.defs_notation, {}).items():
             for name, param in definition.get("properties", {}).items():
                 if "type" in param:
                     self.schema_types[name] = param["type"]

From 0838d6bb040b8218493fad13c5fc33fa355b84af Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Mon, 19 Aug 2024 14:58:27 +0200
Subject: [PATCH 11/63] warning for nf-validation

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

diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py
index 8fe933d102..84bb492cb0 100644
--- a/nf_core/pipelines/lint/nextflow_config.py
+++ b/nf_core/pipelines/lint/nextflow_config.py
@@ -396,6 +396,9 @@ def nextflow_config(self) -> Dict[str, List[str]]:
             elif "nf-validation" not in found_plugins and "nf-schema" not in found_plugins:
                 failed.append("nextflow.config does not contain `nf-validation` or `nf-schema` in the plugins scope")
 
+            if "nf-validation" in found_plugins:
+                warned.append("nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/")
+
     # Check that the default values in nextflow.config match the default values defined in the nextflow_schema.json
     ignore_defaults = []
     for item in ignore_configs:

From 8559c2d6a18624c5096957e6a941011c8725e580 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Mon, 19 Aug 2024 16:54:38 +0200
Subject: [PATCH 12/63] fetch plugin on schema filename setting

---
 nf_core/pipelines/lint/nextflow_config.py |  1 +
 nf_core/pipelines/schema.py               | 81 +++++++++++++++--------
 2 files changed, 54 insertions(+), 28 deletions(-)

diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py
index 84bb492cb0..a5b7cf325f 100644
--- a/nf_core/pipelines/lint/nextflow_config.py
+++ b/nf_core/pipelines/lint/nextflow_config.py
@@ -364,6 +364,7 @@ def nextflow_config(self) -> Dict[str, List[str]]:
             else:
                 failed.append("nextflow.config does not contain configuration profile `test`")
 
+        # Lint for nf-validation and nf-schema
         match_plugins = re.search(r"\bplugins\s*\{([^}]+)}", cleaned_content, re.MULTILINE)
         if not match_plugins:
             failed.append(
diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index c70332beb2..77f421724e 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -5,6 +5,7 @@
 import logging
 import tempfile
 import webbrowser
+import re
 from pathlib import Path
 from typing import Union
 
@@ -32,7 +33,7 @@ def __init__(self):
 
         self.schema = {}
         self.pipeline_dir = ""
-        self.schema_filename = ""
+        self._schema_filename = ""
         self.schema_defaults = {}
         self.schema_types = {}
         self.schema_params = {}
@@ -46,8 +47,46 @@ def __init__(self):
         self.web_schema_build_url = "https://nf-co.re/pipeline_schema_builder"
         self.web_schema_build_web_url = None
         self.web_schema_build_api_url = None
-        self.schema_draft = "https://json-schema.org/draft/2020-12/schema"
-        self.defs_notation = "$defs"
+        self.validation_plugin = None
+        self.schema_draft = None
+        self.defs_notation = None
+
+    # Update the validation plugin code everytime the schema gets changed
+    def set_schema_filename(self, schema: str) -> None:
+        self._schema_filename = schema
+        basepath = "/".join(str(schema).split("/")[:-1])
+        config = f"{basepath}/nextflow.config" if basepath != "" else "nextflow.config"
+        self._update_validation_plugin_from_config(config)
+    
+    def get_schema_filename(self) -> str:
+        return self._schema_filename
+    
+    def del_schema_filename(self) -> None:
+        del self._schema_filename
+
+    schema_filename = property(get_schema_filename, set_schema_filename, del_schema_filename)
+
+    def _update_validation_plugin_from_config(self, config: str) -> None:
+        plugin = "nf-schema"
+        with open(Path(config)) as conf:
+            nf_schema_pattern = re.compile("id\s*[\"']nf-schema", re.MULTILINE)
+            nf_validation_pattern = re.compile("id\s*[\"']nf-validation", re.MULTILINE)
+            config_content = conf.read()
+            if re.search(nf_validation_pattern, config_content):
+                plugin = "nf-validation"
+            elif re.search(nf_schema_pattern, config_content):
+                plugin = "nf-schema"
+            else:
+                log.warning("Could not find nf-schema or nf-validation in the pipeline config. Defaulting to nf-schema")
+            
+        self.validation_plugin = plugin
+        # Previous versions of nf-schema used "defs", but it's advised to use "$defs"
+        if plugin == "nf-schema":
+            self.defs_notation = "$defs"
+            self.schema_draft = "https://json-schema.org/draft/2020-12/schema"
+        else:
+            self.defs_notation = "definitions"
+            self.schema_draft = "https://json-schema.org/draft-07/schema"
 
     def get_schema_path(
         self, path: Union[str, Path], local_only: bool = False, revision: Union[str, None] = None
@@ -120,24 +159,8 @@ def load_schema(self):
         self.schema_params = {}
         if "$schema" not in self.schema:
             raise AssertionError("Schema missing top-level `$schema` attribute")
-        self.schema_draft = self.schema["$schema"]
-        self.defs_notation = self.get_defs_notation()
         log.debug(f"JSON file loaded: {self.schema_filename}")
 
-    def get_defs_notation(self, schema=None):
-        if schema is None:
-            schema = self.schema
-
-        if "$defs" in schema:
-            defs_notation = "$defs"
-        elif "definitions" in schema:
-            defs_notation = "definitions"
-        elif "defs" in schema:
-            # nf-schema v2.0.0 only supported defs. this has been changed to $defs in nf-schema v2.1.0
-            # this line prevents the breakage of schemas created for v2.0.0
-            defs_notation = "defs"
-        return defs_notation
-
     def sanitise_param_default(self, param):
         """
         Given a param, ensure that the default value is the correct variable type
@@ -385,16 +408,15 @@ def validate_schema(self, schema=None):
         if "$schema" not in schema:
             raise AssertionError("Schema missing top-level `$schema` attribute")
         schema_draft = schema["$schema"]
-        if (
-            schema_draft == "https://json-schema.org/draft-07/schema"
-            or schema_draft == "http://json-schema.org/draft-07/schema"
-        ):
+        if self.schema_draft != schema_draft:
+            raise AssertionError(f"Schema is using the wrong draft: {schema_draft}, should be {self.schema_draft}")
+        if self.schema_draft == "https://json-schema.org/draft-07/schema":
             try:
                 jsonschema.Draft7Validator.check_schema(schema)
                 log.debug("JSON Schema Draft7 validated")
             except jsonschema.exceptions.SchemaError as e:
                 raise AssertionError(f"Schema does not validate as Draft 7 JSON Schema:\n {e}")
-        elif schema_draft == "https://json-schema.org/draft/2020-12/schema":
+        elif self.schema_draft == "https://json-schema.org/draft/2020-12/schema":
             try:
                 jsonschema.Draft202012Validator.check_schema(schema)
                 log.debug("JSON Schema Draft2020-12 validated")
@@ -407,18 +429,21 @@ def validate_schema(self, schema=None):
 
         param_keys = list(schema.get("properties", {}).keys())
         num_params = len(param_keys)
-        defs_notation = self.get_defs_notation(schema)
 
-        for d_key, d_schema in schema.get(defs_notation, {}).items():
+        print(self.defs_notation)
+
+        for d_key, d_schema in schema.get(self.defs_notation, {}).items():
+            print(d_key)
+            print(d_schema)
             # Check that this definition is mentioned in allOf
             if "allOf" not in schema:
                 raise AssertionError("Schema has definitions, but no allOf key")
             in_allOf = False
             for allOf in schema.get("allOf", []):
-                if allOf["$ref"] == f"#/{defs_notation}/{d_key}":
+                if allOf["$ref"] == f"#/{self.defs_notation}/{d_key}":
                     in_allOf = True
             if not in_allOf:
-                raise AssertionError(f"Definition subschema `#/{defs_notation}/{d_key}` not included in schema `allOf`")
+                raise AssertionError(f"Definition subschema `#/{self.defs_notation}/{d_key}` not included in schema `allOf`")
 
             # TODO add support for nested parameters
             for d_param_id in d_schema.get("properties", {}):

From 0296f7d8fa6c5cc7a8dac62b450a8babcd77bab7 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Mon, 19 Aug 2024 17:00:33 +0200
Subject: [PATCH 13/63] add a check for defs usage instead of $defs

---
 nf_core/pipelines/schema.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index 77f421724e..9c65f34fde 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -430,11 +430,11 @@ def validate_schema(self, schema=None):
         param_keys = list(schema.get("properties", {}).keys())
         num_params = len(param_keys)
 
-        print(self.defs_notation)
+        # Add a small check for older nf-schema JSON schemas
+        if "defs" in schema:
+            raise AssertionError(f'Using "defs" for schema definitions is not supported. Please use {self.defs_notation} instead')
 
         for d_key, d_schema in schema.get(self.defs_notation, {}).items():
-            print(d_key)
-            print(d_schema)
             # Check that this definition is mentioned in allOf
             if "allOf" not in schema:
                 raise AssertionError("Schema has definitions, but no allOf key")

From 0b8d04f89eb7f348bce87cc93f04d983e48e218f Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Mon, 19 Aug 2024 17:16:31 +0200
Subject: [PATCH 14/63] change all definitions to self.defs_notation

---
 nf_core/pipelines/schema.py | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index 9c65f34fde..9db9457516 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -235,7 +235,7 @@ def save_schema(self, suppress_logging=False):
         """Save a pipeline schema to a file"""
         # Write results to a JSON file
         num_params = len(self.schema.get("properties", {}))
-        num_params += sum(len(d.get("properties", {})) for d in self.schema.get("definitions", {}).values())
+        num_params += sum(len(d.get("properties", {})) for d in self.schema.get(self.defs_notation, {}).values())
         if not suppress_logging:
             log.info(f"Writing schema with {num_params} params: '{self.schema_filename}'")
         dump_json_with_prettier(self.schema_filename, self.schema)
@@ -321,7 +321,7 @@ def validate_default_params(self):
             params_ignore = []
 
         # Go over group keys
-        for group_key, group in schema_no_required.get("definitions", {}).items():
+        for group_key, group in schema_no_required.get(self.defs_notation, {}).items():
             group_properties = group.get("properties")
             for param in group_properties:
                 if param in params_ignore:
@@ -527,9 +527,9 @@ def check_for_input_mimetype(self):
         if "input" not in self.schema_params:
             raise LookupError("Parameter `input` not found in schema")
         # Check that the input parameter is defined in the right place
-        if "input" not in self.schema.get("definitions", {}).get("input_output_options", {}).get("properties", {}):
+        if "input" not in self.schema.get(self.defs_notation, {}).get("input_output_options", {}).get("properties", {}):
             raise LookupError("Parameter `input` is not defined in the correct subschema (input_output_options)")
-        input_entry = self.schema["definitions"]["input_output_options"]["properties"]["input"]
+        input_entry = self.schema[self.defs_notation]["input_output_options"]["properties"]["input"]
         if "mimetype" not in input_entry:
             return None
         mimetype = input_entry["mimetype"]
@@ -581,7 +581,7 @@ def schema_to_markdown(self, columns):
         out = f"# {self.schema['title']}\n\n"
         out += f"{self.schema['description']}\n"
         # Grouped parameters
-        for definition in self.schema.get("definitions", {}).values():
+        for definition in self.schema.get(self.defs_notation, {}).values():
             out += f"\n## {definition.get('title', {})}\n\n"
             out += f"{definition.get('description', '')}\n\n"
             required = definition.get("required", [])
@@ -763,15 +763,15 @@ def remove_schema_empty_definitions(self):
         """
         # Identify and remove empty definitions from the schema
         empty_definitions = []
-        for d_key, d_schema in list(self.schema.get("definitions", {}).items()):
+        for d_key, d_schema in list(self.schema.get(self.defs_notation, {}).items()):
             if not d_schema.get("properties"):
-                del self.schema["definitions"][d_key]
+                del self.schema[self.defs_notation][d_key]
                 empty_definitions.append(d_key)
                 log.warning(f"Removing empty group: '{d_key}'")
 
         # Remove "allOf" group with empty definitions from the schema
         for d_key in empty_definitions:
-            allOf = {"$ref": f"#/definitions/{d_key}"}
+            allOf = {"$ref": f"#/{self.defs_notation}/{d_key}"}
             if allOf in self.schema.get("allOf", []):
                 self.schema["allOf"].remove(allOf)
 
@@ -780,8 +780,8 @@ def remove_schema_empty_definitions(self):
             del self.schema["allOf"]
 
         # If we don't have anything left in "definitions", remove it
-        if self.schema.get("definitions") == {}:
-            del self.schema["definitions"]
+        if self.schema.get(self.defs_notation) == {}:
+            del self.schema[self.defs_notation]
 
     def remove_schema_notfound_configs(self):
         """
@@ -791,9 +791,9 @@ def remove_schema_notfound_configs(self):
         # Top-level properties
         self.schema, params_removed = self.remove_schema_notfound_configs_single_schema(self.schema)
         # Sub-schemas in definitions
-        for d_key, definition in self.schema.get("definitions", {}).items():
+        for d_key, definition in self.schema.get(self.defs_notation, {}).items():
             cleaned_schema, p_removed = self.remove_schema_notfound_configs_single_schema(definition)
-            self.schema["definitions"][d_key] = cleaned_schema
+            self.schema[self.defs_notation][d_key] = cleaned_schema
             params_removed.extend(p_removed)
 
         return params_removed

From 544381310c6e5ac57664524f63105441246c34fd Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Mon, 19 Aug 2024 18:33:52 +0200
Subject: [PATCH 15/63] migrate template part 1

---
 nf_core/pipeline-template/conf/colors.config  |  61 ++++++++
 nf_core/pipeline-template/nextflow.config     |  44 ++++--
 .../pipeline-template/nextflow_schema.json    |  55 +++----
 .../utils_nfcore_pipeline_pipeline/main.nf    |  17 +-
 .../nf-core/utils_nfcore_pipeline/main.nf     |  46 ------
 .../nf-core/utils_nfvalidation_plugin/main.nf |  25 +--
 .../tests/main.nf.test                        | 145 +-----------------
 .../tests/nextflow.config                     |   1 +
 .../pipeline-template/workflows/pipeline.nf   |   2 +-
 9 files changed, 130 insertions(+), 266 deletions(-)
 create mode 100644 nf_core/pipeline-template/conf/colors.config
 create mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow.config

diff --git a/nf_core/pipeline-template/conf/colors.config b/nf_core/pipeline-template/conf/colors.config
new file mode 100644
index 0000000000..00f2963267
--- /dev/null
+++ b/nf_core/pipeline-template/conf/colors.config
@@ -0,0 +1,61 @@
+// For now, there is no easy way to set monochromeLogs
+colors {
+    // Reset / Meta
+    reset      = "\033[0m"
+    bold       = "\033[1m"
+    dim        = "\033[2m"
+    underlined = "\033[4m"
+    blink      = "\033[5m"
+    reverse    = "\033[7m"
+    hidden     = "\033[8m"
+
+    // Regular Colors
+    black      = "\033[0;30m"
+    red        = "\033[0;31m"
+    green      = "\033[0;32m"
+    yellow     = "\033[0;33m"
+    blue       = "\033[0;34m"
+    purple     = "\033[0;35m"
+    cyan       = "\033[0;36m"
+    white      = "\033[0;37m"
+
+    // Bold
+    bblack     = "\033[1;30m"
+    bred       = "\033[1;31m"
+    bgreen     = "\033[1;32m"
+    byellow    = "\033[1;33m"
+    bblue      = "\033[1;34m"
+    bpurple    = "\033[1;35m"
+    bcyan      = "\033[1;36m"
+    bwhite     = "\033[1;37m"
+
+    // Underline
+    ublack     = "\033[4;30m"
+    ured       = "\033[4;31m"
+    ugreen     = "\033[4;32m"
+    uyellow    = "\033[4;33m"
+    ublue      = "\033[4;34m"
+    upurple    = "\033[4;35m"
+    ucyan      = "\033[4;36m"
+    uwhite     = "\033[4;37m"
+
+    // High Intensity
+    iblack     = "\033[0;90m"
+    ired       = "\033[0;91m"
+    igreen     = "\033[0;92m"
+    iyellow    = "\033[0;93m"
+    iblue      = "\033[0;94m"
+    ipurple    = "\033[0;95m"
+    icyan      = "\033[0;96m"
+    iwhite     = "\033[0;97m"
+
+    // Bold High Intensity
+    biblack    = "\033[1;90m"
+    bired      = "\033[1;91m"
+    bigreen    = "\033[1;92m"
+    biyellow   = "\033[1;93m"
+    biblue     = "\033[1;94m"
+    bipurple   = "\033[1;95m"
+    bicyan     = "\033[1;96m"
+    biwhite    = "\033[1;97m"
+}
\ No newline at end of file
diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 0469d6cfec..3d3841ba49 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -38,6 +38,8 @@ params {
     monochrome_logs              = false
     hook_url                     = null
     help                         = false
+    helpFull                     = false
+    showHidden                   = false
     version                      = false
     pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
 
@@ -59,10 +61,6 @@ params {
     max_time                   = '240.h'
 
     // Schema validation default options
-    validationFailUnrecognisedParams = false
-    validationLenientMode            = false
-    validationSchemaIgnoreParams     = 'genomes,igenomes_base'
-    validationShowHiddenParams       = false
     validate_params                  = true
 
 }
@@ -200,11 +198,6 @@ podman.registry       = 'quay.io'
 singularity.registry  = 'quay.io'
 charliecloud.registry = 'quay.io'
 
-// Nextflow plugins
-plugins {
-    id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet
-}
-
 {% if igenomes -%}
 // Load igenomes.config if required
 if (!params.igenomes_ignore) {
@@ -267,6 +260,39 @@ manifest {
     doi             = ''
 }
 
+// Nextflow plugins
+plugins {
+    id 'nf-schema@2.1.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+}
+
+includeConfig "conf/colors.config"
+
+validation {
+    parametersSchema = "${projectDir}/nextflow_schema.json"
+    help {
+        enabled = true
+        command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
+        beforeText = """
+-${colors.dim}----------------------------------------------------${colors.reset}-
+                                        ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset}
+${colors.blue}        ___     __   __   __   ___     ${colors.green}/,-._.--~\'${colors.reset}
+${colors.blue}  |\\ | |__  __ /  ` /  \\ |__) |__         ${colors.yellow}}  {${colors.reset}
+${colors.blue}  | \\| |       \\__, \\__/ |  \\ |___     ${colors.green}\\`-._,-`-,${colors.reset}
+                                        ${colors.green}`._,._,\'${colors.reset}
+${colors.purple}  ${manifest.name} ${manifest.version}${colors.reset}
+-${colors.dim}----------------------------------------------------${colors.reset}-
+"""
+        afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "  https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
+* The nf-core framework 
+  https://doi.org/10.1038/s41587-020-0439-x
+
+* Software dependencies
+  https://github.com/${manifest.name}/blob/master/CITATIONS.md
+"""
+    }
+}
+
+
 // Load modules.config for DSL2 module specific options
 includeConfig 'conf/modules.config'
 
diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json
index 4a1a22c3ee..14120bbabc 100644
--- a/nf_core/pipeline-template/nextflow_schema.json
+++ b/nf_core/pipeline-template/nextflow_schema.json
@@ -1,10 +1,10 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "$id": "https://raw.githubusercontent.com/{{ name }}/master/nextflow_schema.json",
     "title": "{{ name }} pipeline parameters",
     "description": "{{ description }}",
     "type": "object",
-    "definitions": {
+    "$defs": {
         "input_output_options": {
             "title": "Input/output options",
             "type": "object",
@@ -73,6 +73,20 @@
                     "fa_icon": "fas fa-ban",
                     "hidden": true,
                     "help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`."
+                },
+                "igenomes_base": {
+                    "type": "string",
+                    "format": "directory-path",
+                    "description": "The base path to the igenomes reference files",
+                    "fa_icon": "fas fa-ban",
+                    "hidden": true,
+                    "default": "s3://ngi-igenomes/igenomes/"
+                },
+                "genomes": {
+                    "type": "object",
+                    "description": "An object containing all reference data availabe in igenomes",
+                    "fa_icon": "fas fa-ban",
+                    "hidden": true
                 }
             }
         },
@@ -169,12 +183,6 @@
             "description": "Less common options for the pipeline, typically set in a config file.",
             "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
             "properties": {
-                "help": {
-                    "type": "boolean",
-                    "description": "Display help text.",
-                    "fa_icon": "fas fa-question-circle",
-                    "hidden": true
-                },
                 "version": {
                     "type": "boolean",
                     "description": "Display version and exit.",
@@ -253,27 +261,6 @@
                     "fa_icon": "fas fa-check-square",
                     "hidden": true
                 },
-                "validationShowHiddenParams": {
-                    "type": "boolean",
-                    "fa_icon": "far fa-eye-slash",
-                    "description": "Show all params when using `--help`",
-                    "hidden": true,
-                    "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
-                },
-                "validationFailUnrecognisedParams": {
-                    "type": "boolean",
-                    "fa_icon": "far fa-check-circle",
-                    "description": "Validation of parameters fails when an unrecognised parameter is found.",
-                    "hidden": true,
-                    "help_text": "By default, when an unrecognised parameter is found, it returns a warinig."
-                },
-                "validationLenientMode": {
-                    "type": "boolean",
-                    "fa_icon": "far fa-check-circle",
-                    "description": "Validation of parameters in lenient more.",
-                    "hidden": true,
-                    "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)."
-                },
                 "pipelines_testdata_base_path": {
                     "type": "string",
                     "fa_icon": "far fa-check-circle",
@@ -286,19 +273,19 @@
     },
     "allOf": [
         {
-            "$ref": "#/definitions/input_output_options"
+            "$ref": "#/$defs/input_output_options"
         },
         {% if igenomes %}{
-            "$ref": "#/definitions/reference_genome_options"
+            "$ref": "#/$defs/reference_genome_options"
         },{% endif %}
         {% if nf_core_configs %}{
-            "$ref": "#/definitions/institutional_config_options"
+            "$ref": "#/$defs/institutional_config_options"
         },{% endif %}
         {
-            "$ref": "#/definitions/max_job_request_options"
+            "$ref": "#/$defs/max_job_request_options"
         },
         {
-            "$ref": "#/definitions/generic_options"
+            "$ref": "#/$defs/generic_options"
         }
     ]
 }
diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
index 72c9be85eb..c83d2ae0cb 100644
--- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
@@ -9,8 +9,8 @@
 */
 
 include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin'
-include { paramsSummaryMap          } from 'plugin/nf-validation'
-include { fromSamplesheet           } from 'plugin/nf-validation'
+include { paramsSummaryMap          } from 'plugin/nf-schema'
+include { samplesheetToList         } from 'plugin/nf-schema'
 include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
 include { completionEmail           } from '../../nf-core/utils_nfcore_pipeline'
 include { completionSummary         } from '../../nf-core/utils_nfcore_pipeline'
@@ -30,7 +30,6 @@ workflow PIPELINE_INITIALISATION {
 
     take:
     version           // boolean: Display version and exit
-    help              // boolean: Display help text
     validate_params   // boolean: Boolean whether to validate parameters against the schema at runtime
     monochrome_logs   // boolean: Do not use coloured log outputs
     nextflow_cli_args //   array: List of positional nextflow CLI args
@@ -54,16 +53,8 @@ workflow PIPELINE_INITIALISATION {
     //
     // Validate parameters and generate parameter summary to stdout
     //
-    pre_help_text = nfCoreLogo(monochrome_logs)
-    post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(monochrome_logs)
-    def String workflow_command = "nextflow run ${workflow.manifest.name} -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
     UTILS_NFVALIDATION_PLUGIN (
-        help,
-        workflow_command,
-        pre_help_text,
-        post_help_text,
-        validate_params,
-        "nextflow_schema.json"
+        validate_params
     )
 
     //
@@ -84,7 +75,7 @@ workflow PIPELINE_INITIALISATION {
     // Create channel from input file provided through params.input
     //
     Channel
-        .fromSamplesheet("input")
+        .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
         .map {
             meta, fastq_1, fastq_2 ->
                 if (!fastq_2) {
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index 14558c3927..a5dcd5f83d 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -61,25 +61,6 @@ def checkProfileProvided(nextflow_cli_args) {
     }
 }
 
-//
-// Citation string for pipeline
-//
-def workflowCitation() {
-    def temp_doi_ref = ""
-    String[] manifest_doi = workflow.manifest.doi.tokenize(",")
-    // Using a loop to handle multiple DOIs
-    // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
-    // Removing ` ` since the manifest.doi is a string and not a proper list
-    for (String doi_ref: manifest_doi) temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
-    return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
-        "* The pipeline\n" +
-        temp_doi_ref + "\n" +
-        "* The nf-core framework\n" +
-        "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
-        "* Software dependencies\n" +
-        "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
-}
-
 //
 // Generate workflow version string
 //
@@ -157,33 +138,6 @@ def paramsSummaryMultiqc(summary_params) {
     return yaml_file_text
 }
 
-//
-// nf-core logo
-//
-def nfCoreLogo(monochrome_logs=true) {
-    Map colors = logColours(monochrome_logs)
-    String.format(
-        """\n
-        ${dashedLine(monochrome_logs)}
-                                                ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset}
-        ${colors.blue}        ___     __   __   __   ___     ${colors.green}/,-._.--~\'${colors.reset}
-        ${colors.blue}  |\\ | |__  __ /  ` /  \\ |__) |__         ${colors.yellow}}  {${colors.reset}
-        ${colors.blue}  | \\| |       \\__, \\__/ |  \\ |___     ${colors.green}\\`-._,-`-,${colors.reset}
-                                                ${colors.green}`._,._,\'${colors.reset}
-        ${colors.purple}  ${workflow.manifest.name} ${getWorkflowVersion()}${colors.reset}
-        ${dashedLine(monochrome_logs)}
-        """.stripIndent()
-    )
-}
-
-//
-// Return dashed line
-//
-def dashedLine(monochrome_logs=true) {
-    Map colors = logColours(monochrome_logs)
-    return "-${colors.dim}----------------------------------------------------${colors.reset}-"
-}
-
 //
 // ANSII colours used for terminal logging
 //
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
index 2585b65d1b..453894a64a 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
@@ -8,9 +8,8 @@
 ========================================================================================
 */
 
-include { paramsHelp         } from 'plugin/nf-validation'
-include { paramsSummaryLog   } from 'plugin/nf-validation'
-include { validateParameters } from 'plugin/nf-validation'
+include { paramsSummaryLog   } from 'plugin/nf-schema'
+include { validateParameters } from 'plugin/nf-schema'
 
 /*
 ========================================================================================
@@ -21,12 +20,7 @@ include { validateParameters } from 'plugin/nf-validation'
 workflow UTILS_NFVALIDATION_PLUGIN {
 
     take:
-    print_help       // boolean: print help
-    workflow_command //  string: default commmand used to run pipeline
-    pre_help_text    //  string: string to be printed before help text and summary log
-    post_help_text   //  string: string to be printed after help text and summary log
     validate_params  // boolean: validate parameters
-    schema_filename  //    path: JSON schema file, null to use default value
 
     main:
 
@@ -37,24 +31,11 @@ workflow UTILS_NFVALIDATION_PLUGIN {
     post_help_text   = post_help_text   ?: ''
     workflow_command = workflow_command ?: ''
 
-    //
-    // Print help message if needed
-    //
-    if (print_help) {
-        log.info pre_help_text + paramsHelp(workflow_command, parameters_schema: schema_filename) + post_help_text
-        System.exit(0)
-    }
-
-    //
-    // Print parameter summary to stdout
-    //
-    log.info pre_help_text + paramsSummaryLog(workflow, parameters_schema: schema_filename) + post_help_text
-
     //
     // Validate parameters relative to the parameter JSON schema
     //
     if (validate_params){
-        validateParameters(parameters_schema: schema_filename)
+        validateParameters()
     }
 
     emit:
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
index 5784a33f2f..354b817545 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
@@ -10,30 +10,21 @@ nextflow_workflow {
     tag "utils_nfvalidation_plugin"
     tag "subworkflows/utils_nfvalidation_plugin"
 
+    config "./nextflow.config"
+
     test("Should run nothing") {
 
         when {
 
             params {
-                monochrome_logs = true
                 test_data       = ''
             }
 
             workflow {
                 """
-                help             = false
-                workflow_command = null
-                pre_help_text    = null
-                post_help_text   = null
                 validate_params  = false
-                schema_filename  = "$moduleTestDir/nextflow_schema.json"
 
-                input[0] = help
-                input[1] = workflow_command
-                input[2] = pre_help_text
-                input[3] = post_help_text
-                input[4] = validate_params
-                input[5] = schema_filename
+                input[0] = validate_params
                 """
             }
         }
@@ -45,147 +36,19 @@ nextflow_workflow {
         }
     }
 
-    test("Should run help") {
-
-
-        when {
-
-            params {
-                monochrome_logs = true
-                test_data       = ''
-            }
-            workflow {
-                """
-                help             = true
-                workflow_command = null
-                pre_help_text    = null
-                post_help_text   = null
-                validate_params  = false
-                schema_filename  = "$moduleTestDir/nextflow_schema.json"
-
-                input[0] = help
-                input[1] = workflow_command
-                input[2] = pre_help_text
-                input[3] = post_help_text
-                input[4] = validate_params
-                input[5] = schema_filename
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert workflow.exitStatus == 0 },
-                { assert workflow.stdout.any { it.contains('Input/output options') } },
-                { assert workflow.stdout.any { it.contains('--outdir') } }
-            )
-        }
-    }
-
-    test("Should run help with command") {
-
-        when {
-
-            params {
-                monochrome_logs = true
-                test_data       = ''
-            }
-            workflow {
-                """
-                help             = true
-                workflow_command = "nextflow run noorg/doesntexist"
-                pre_help_text    = null
-                post_help_text   = null
-                validate_params  = false
-                schema_filename  = "$moduleTestDir/nextflow_schema.json"
-
-                input[0] = help
-                input[1] = workflow_command
-                input[2] = pre_help_text
-                input[3] = post_help_text
-                input[4] = validate_params
-                input[5] = schema_filename
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert workflow.exitStatus == 0 },
-                { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } },
-                { assert workflow.stdout.any { it.contains('Input/output options') } },
-                { assert workflow.stdout.any { it.contains('--outdir') } }
-            )
-        }
-    }
-
-    test("Should run help with extra text") {
-
-
-        when {
-
-            params {
-                monochrome_logs = true
-                test_data       = ''
-            }
-            workflow {
-                """
-                help             = true
-                workflow_command = "nextflow run noorg/doesntexist"
-                pre_help_text    = "pre-help-text"
-                post_help_text   = "post-help-text"
-                validate_params  = false
-                schema_filename  = "$moduleTestDir/nextflow_schema.json"
-
-                input[0] = help
-                input[1] = workflow_command
-                input[2] = pre_help_text
-                input[3] = post_help_text
-                input[4] = validate_params
-                input[5] = schema_filename
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert workflow.exitStatus == 0 },
-                { assert workflow.stdout.any { it.contains('pre-help-text') } },
-                { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } },
-                { assert workflow.stdout.any { it.contains('Input/output options') } },
-                { assert workflow.stdout.any { it.contains('--outdir') } },
-                { assert workflow.stdout.any { it.contains('post-help-text') } }
-            )
-        }
-    }
-
     test("Should validate params") {
 
         when {
 
             params {
-                monochrome_logs = true
                 test_data       = ''
                 outdir          = 1
             }
             workflow {
                 """
-                help             = false
-                workflow_command = null
-                pre_help_text    = null
-                post_help_text   = null
                 validate_params  = true
-                schema_filename  = "$moduleTestDir/nextflow_schema.json"
 
-                input[0] = help
-                input[1] = workflow_command
-                input[2] = pre_help_text
-                input[3] = post_help_text
-                input[4] = validate_params
-                input[5] = schema_filename
+                input[0] = validate_params
                 """
             }
         }
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow.config b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow.config
new file mode 100644
index 0000000000..8d047ed59e
--- /dev/null
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow.config
@@ -0,0 +1 @@
+validation.monochromeLogs = true
\ No newline at end of file
diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf
index d98c392f0c..4bb0913211 100644
--- a/nf_core/pipeline-template/workflows/pipeline.nf
+++ b/nf_core/pipeline-template/workflows/pipeline.nf
@@ -6,7 +6,7 @@
 
 include { FASTQC                 } from '../modules/nf-core/fastqc/main'
 {% if multiqc %}include { MULTIQC                } from '../modules/nf-core/multiqc/main'{% endif %}
-include { paramsSummaryMap       } from 'plugin/nf-validation'
+include { paramsSummaryMap       } from 'plugin/nf-schema'
 {% if multiqc %}include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pipeline'{% endif %}
 include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 {% if citations or multiqc %}include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'{% endif %}

From 5519c83d5b582af797ff4ae242fa98113bbe847a Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 20 Aug 2024 15:24:51 +0200
Subject: [PATCH 16/63] some small updates for the new release

---
 nf_core/pipeline-template/conf/colors.config  | 61 -------------------
 nf_core/pipeline-template/modules.json        |  4 +-
 nf_core/pipeline-template/nextflow.config     | 22 ++++---
 .../nf-core/utils_nfschema_plugin/main.nf     | 32 ++++++++++
 .../nf-core/utils_nfschema_plugin/meta.yml    | 22 +++++++
 .../tests/main.nf.test                        | 27 ++++----
 .../tests/nextflow.config                     |  8 +++
 .../tests/nextflow_schema.json                |  8 +--
 .../nf-core/utils_nfvalidation_plugin/main.nf | 43 -------------
 .../utils_nfvalidation_plugin/meta.yml        | 44 -------------
 .../tests/nextflow.config                     |  1 -
 .../utils_nfvalidation_plugin/tests/tags.yml  |  2 -
 12 files changed, 93 insertions(+), 181 deletions(-)
 delete mode 100644 nf_core/pipeline-template/conf/colors.config
 create mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/main.nf
 create mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/meta.yml
 rename nf_core/pipeline-template/subworkflows/nf-core/{utils_nfvalidation_plugin => utils_nfschema_plugin}/tests/main.nf.test (62%)
 create mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
 rename nf_core/pipeline-template/subworkflows/nf-core/{utils_nfvalidation_plugin => utils_nfschema_plugin}/tests/nextflow_schema.json (95%)
 delete mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
 delete mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml
 delete mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow.config
 delete mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml

diff --git a/nf_core/pipeline-template/conf/colors.config b/nf_core/pipeline-template/conf/colors.config
deleted file mode 100644
index 00f2963267..0000000000
--- a/nf_core/pipeline-template/conf/colors.config
+++ /dev/null
@@ -1,61 +0,0 @@
-// For now, there is no easy way to set monochromeLogs
-colors {
-    // Reset / Meta
-    reset      = "\033[0m"
-    bold       = "\033[1m"
-    dim        = "\033[2m"
-    underlined = "\033[4m"
-    blink      = "\033[5m"
-    reverse    = "\033[7m"
-    hidden     = "\033[8m"
-
-    // Regular Colors
-    black      = "\033[0;30m"
-    red        = "\033[0;31m"
-    green      = "\033[0;32m"
-    yellow     = "\033[0;33m"
-    blue       = "\033[0;34m"
-    purple     = "\033[0;35m"
-    cyan       = "\033[0;36m"
-    white      = "\033[0;37m"
-
-    // Bold
-    bblack     = "\033[1;30m"
-    bred       = "\033[1;31m"
-    bgreen     = "\033[1;32m"
-    byellow    = "\033[1;33m"
-    bblue      = "\033[1;34m"
-    bpurple    = "\033[1;35m"
-    bcyan      = "\033[1;36m"
-    bwhite     = "\033[1;37m"
-
-    // Underline
-    ublack     = "\033[4;30m"
-    ured       = "\033[4;31m"
-    ugreen     = "\033[4;32m"
-    uyellow    = "\033[4;33m"
-    ublue      = "\033[4;34m"
-    upurple    = "\033[4;35m"
-    ucyan      = "\033[4;36m"
-    uwhite     = "\033[4;37m"
-
-    // High Intensity
-    iblack     = "\033[0;90m"
-    ired       = "\033[0;91m"
-    igreen     = "\033[0;92m"
-    iyellow    = "\033[0;93m"
-    iblue      = "\033[0;94m"
-    ipurple    = "\033[0;95m"
-    icyan      = "\033[0;96m"
-    iwhite     = "\033[0;97m"
-
-    // Bold High Intensity
-    biblack    = "\033[1;90m"
-    bired      = "\033[1;91m"
-    bigreen    = "\033[1;92m"
-    biyellow   = "\033[1;93m"
-    biblue     = "\033[1;94m"
-    bipurple   = "\033[1;95m"
-    bicyan     = "\033[1;96m"
-    biwhite    = "\033[1;97m"
-}
\ No newline at end of file
diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json
index eb9391b29a..1a3b96490d 100644
--- a/nf_core/pipeline-template/modules.json
+++ b/nf_core/pipeline-template/modules.json
@@ -30,9 +30,9 @@
                         "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
                         "installed_by": ["subworkflows"]
                     },
-                    "utils_nfvalidation_plugin": {
+                    "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "a3e87febb28bd0461c22a917c5b2c1492053ef85",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 3d3841ba49..346292c980 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -265,22 +265,20 @@ plugins {
     id 'nf-schema@2.1.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
 }
 
-includeConfig "conf/colors.config"
-
 validation {
     parametersSchema = "${projectDir}/nextflow_schema.json"
     help {
         enabled = true
         command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
         beforeText = """
--${colors.dim}----------------------------------------------------${colors.reset}-
-                                        ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset}
-${colors.blue}        ___     __   __   __   ___     ${colors.green}/,-._.--~\'${colors.reset}
-${colors.blue}  |\\ | |__  __ /  ` /  \\ |__) |__         ${colors.yellow}}  {${colors.reset}
-${colors.blue}  | \\| |       \\__, \\__/ |  \\ |___     ${colors.green}\\`-._,-`-,${colors.reset}
-                                        ${colors.green}`._,._,\'${colors.reset}
-${colors.purple}  ${manifest.name} ${manifest.version}${colors.reset}
--${colors.dim}----------------------------------------------------${colors.reset}-
+-\033[2m----------------------------------------------------\033[0m-
+                                        \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m
+\033[0;34m        ___     __   __   __   ___     \033[0;32m/,-._.--~\'\033[0m
+\033[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \033[0;33m}  {\033[0m
+\033[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \033[0;32m\\`-._,-`-,\033[0m
+                                        \033[0;32m`._,._,\'\033[0m
+\033[0;35m  ${manifest.name} ${manifest.version}\033[0m
+-\033[2m----------------------------------------------------\033[0m-
 """
         afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "  https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
 * The nf-core framework 
@@ -290,6 +288,10 @@ ${colors.purple}  ${manifest.name} ${manifest.version}${colors.reset}
   https://github.com/${manifest.name}/blob/master/CITATIONS.md
 """
     }
+    summary {
+        beforeText = validation.help.beforeText
+        afterText = validation.help.afterText
+    }
 }
 
 
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/main.nf
new file mode 100644
index 0000000000..5d1dc7c928
--- /dev/null
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/main.nf
@@ -0,0 +1,32 @@
+//
+// Subworkflow that uses the nf-schema plugin to validate parameters and render the parameter summary
+//
+
+include { paramsSummaryLog   } from 'plugin/nf-schema'
+include { validateParameters } from 'plugin/nf-schema'
+
+workflow UTILS_NFSCHEMA_PLUGIN {
+
+    take:
+    validate_params // boolean: validate the parameters
+
+    main:
+
+    //
+    // Print parameter summary to stdout. This will display the parameters
+    // that differ from the default given in the JSON schema
+    //
+    log.info paramsSummaryLog(workflow)
+
+    //
+    // Validate the parameters using nextflow_schema.json or the schema
+    // given via the validation.parametersSchema configuration option
+    //
+    if(validate_params) {
+        validateParameters()
+    }
+
+    emit:
+    dummy_emit = true
+}
+
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/meta.yml b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/meta.yml
new file mode 100644
index 0000000000..90b8cb1898
--- /dev/null
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/meta.yml
@@ -0,0 +1,22 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "utils_nfschema_plugin"
+description: Run nf-schema to validate parameters and create a summary of changed parameters
+keywords:
+  - validation
+  - JSON schema
+  - plugin
+  - parameters
+  - summary
+components: []
+input:
+  - validate_params:
+      type: boolean
+      description: Validate the parameters and error if invalid.
+output:
+  - dummy_emit:
+      type: boolean
+      description: Dummy emit to make nf-core subworkflows lint happy
+authors:
+  - "@nvnieuwk"
+maintainers:
+  - "@nvnieuwk"
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
similarity index 62%
rename from nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
rename to nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
index 354b817545..703d3a9b86 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
@@ -1,14 +1,14 @@
+// TODO nf-core: Once you have added the required tests, please run the following command to build this file:
+// nf-core subworkflows test utils_nfschema_plugin
 nextflow_workflow {
 
-    name "Test Workflow UTILS_NFVALIDATION_PLUGIN"
+    name "Test Subworkflow UTILS_NFSCHEMA_PLUGIN"
     script "../main.nf"
-    workflow "UTILS_NFVALIDATION_PLUGIN"
+    workflow "UTILS_NFSCHEMA_PLUGIN"
+
     tag "subworkflows"
     tag "subworkflows_nfcore"
-    tag "plugin/nf-validation"
-    tag "'plugin/nf-validation'"
-    tag "utils_nfvalidation_plugin"
-    tag "subworkflows/utils_nfvalidation_plugin"
+    tag "subworkflows/utils_nfschema_plugin"
 
     config "./nextflow.config"
 
@@ -17,13 +17,12 @@ nextflow_workflow {
         when {
 
             params {
-                test_data       = ''
+                test_data   = ''
             }
 
             workflow {
                 """
-                validate_params  = false
-
+                validate_params = false
                 input[0] = validate_params
                 """
             }
@@ -41,13 +40,13 @@ nextflow_workflow {
         when {
 
             params {
-                test_data       = ''
-                outdir          = 1
+                test_data   = ''
+                outdir      = 1
             }
+
             workflow {
                 """
-                validate_params  = true
-
+                validate_params = true
                 input[0] = validate_params
                 """
             }
@@ -56,7 +55,7 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.failed },
-                { assert workflow.stdout.any { it.contains('ERROR ~ ERROR: Validation of pipeline parameters failed!') } }
+                { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } }
             )
         }
     }
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
new file mode 100644
index 0000000000..0907ac58f0
--- /dev/null
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
@@ -0,0 +1,8 @@
+plugins {
+    id "nf-schema@2.1.0"
+}
+
+validation {
+    parametersSchema = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
+    monochromeLogs = true
+}
\ No newline at end of file
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json
similarity index 95%
rename from nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json
rename to nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json
index 7626c1c93e..331e0d2f44 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json
@@ -1,10 +1,10 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json",
     "title": ". pipeline parameters",
     "description": "",
     "type": "object",
-    "definitions": {
+    "$defs": {
         "input_output_options": {
             "title": "Input/output options",
             "type": "object",
@@ -87,10 +87,10 @@
     },
     "allOf": [
         {
-            "$ref": "#/definitions/input_output_options"
+            "$ref": "#/$defs/input_output_options"
         },
         {
-            "$ref": "#/definitions/generic_options"
+            "$ref": "#/$defs/generic_options"
         }
     ]
 }
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
deleted file mode 100644
index 453894a64a..0000000000
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
+++ /dev/null
@@ -1,43 +0,0 @@
-//
-// Subworkflow that uses the nf-validation plugin to render help text and parameter summary
-//
-
-/*
-========================================================================================
-    IMPORT NF-VALIDATION PLUGIN
-========================================================================================
-*/
-
-include { paramsSummaryLog   } from 'plugin/nf-schema'
-include { validateParameters } from 'plugin/nf-schema'
-
-/*
-========================================================================================
-    SUBWORKFLOW DEFINITION
-========================================================================================
-*/
-
-workflow UTILS_NFVALIDATION_PLUGIN {
-
-    take:
-    validate_params  // boolean: validate parameters
-
-    main:
-
-    log.debug "Using schema file: ${schema_filename}"
-
-    // Default values for strings
-    pre_help_text    = pre_help_text    ?: ''
-    post_help_text   = post_help_text   ?: ''
-    workflow_command = workflow_command ?: ''
-
-    //
-    // Validate parameters relative to the parameter JSON schema
-    //
-    if (validate_params){
-        validateParameters()
-    }
-
-    emit:
-    dummy_emit = true
-}
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml
deleted file mode 100644
index 3d4a6b04f5..0000000000
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml
+++ /dev/null
@@ -1,44 +0,0 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
-name: "UTILS_NFVALIDATION_PLUGIN"
-description: Use nf-validation to initiate and validate a pipeline
-keywords:
-  - utility
-  - pipeline
-  - initialise
-  - validation
-components: []
-input:
-  - print_help:
-      type: boolean
-      description: |
-        Print help message and exit
-  - workflow_command:
-      type: string
-      description: |
-        The command to run the workflow e.g. "nextflow run main.nf"
-  - pre_help_text:
-      type: string
-      description: |
-        Text to print before the help message
-  - post_help_text:
-      type: string
-      description: |
-        Text to print after the help message
-  - validate_params:
-      type: boolean
-      description: |
-        Validate the parameters and error if invalid.
-  - schema_filename:
-      type: string
-      description: |
-        The filename of the schema to validate against.
-output:
-  - dummy_emit:
-      type: boolean
-      description: |
-        Dummy emit to make nf-core subworkflows lint happy
-authors:
-  - "@adamrtalbot"
-maintainers:
-  - "@adamrtalbot"
-  - "@maxulysse"
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow.config b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow.config
deleted file mode 100644
index 8d047ed59e..0000000000
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow.config
+++ /dev/null
@@ -1 +0,0 @@
-validation.monochromeLogs = true
\ No newline at end of file
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml
deleted file mode 100644
index 60b1cfff49..0000000000
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-subworkflows/utils_nfvalidation_plugin:
-  - subworkflows/nf-core/utils_nfvalidation_plugin/**

From 171640b62dddcb81feddced4f674df88c47654ab Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 20 Aug 2024 16:13:59 +0200
Subject: [PATCH 17/63] some more small updates to the template

---
 nf_core/pipeline-template/nextflow.config                     | 2 +-
 .../subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 346292c980..ef067dcfab 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -255,7 +255,7 @@ manifest {
     homePage        = 'https://github.com/{{ name }}'
     description     = """{{ description }}"""
     mainScript      = 'main.nf'
-    nextflowVersion = '!>=23.04.0'
+    nextflowVersion = '!>=23.10.0'
     version         = '{{ version }}'
     doi             = ''
 }
diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
index c83d2ae0cb..a994cfd584 100644
--- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
@@ -8,7 +8,7 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin'
+include { UTILS_NFSCHEMA_PLUGIN     } from '../../nf-core/utils_nfschema_plugin'
 include { paramsSummaryMap          } from 'plugin/nf-schema'
 include { samplesheetToList         } from 'plugin/nf-schema'
 include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
@@ -53,7 +53,7 @@ workflow PIPELINE_INITIALISATION {
     //
     // Validate parameters and generate parameter summary to stdout
     //
-    UTILS_NFVALIDATION_PLUGIN (
+    UTILS_NFSCHEMA_PLUGIN (
         validate_params
     )
 

From 249b3da383f17ab0beecfeb9e8346619edaf6776 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 20 Aug 2024 16:59:22 +0200
Subject: [PATCH 18/63] update handling of ignored parameters

---
 .../.github/workflows/ci.yml                  |  2 +-
 nf_core/pipeline-template/README.md           |  2 +-
 nf_core/pipelines/lint/nextflow_config.py     | 15 +++++--------
 nf_core/pipelines/schema.py                   | 22 ++++++++++++++-----
 4 files changed, 23 insertions(+), 18 deletions(-)

diff --git a/nf_core/pipeline-template/.github/workflows/ci.yml b/nf_core/pipeline-template/.github/workflows/ci.yml
index 6b2547765d..63fa99cec8 100644
--- a/nf_core/pipeline-template/.github/workflows/ci.yml
+++ b/nf_core/pipeline-template/.github/workflows/ci.yml
@@ -24,7 +24,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "23.04.0"
+          - "23.10.0"
           - "latest-everything"
     steps:
       - name: Check out pipeline code
diff --git a/nf_core/pipeline-template/README.md b/nf_core/pipeline-template/README.md
index 7718d2e5f8..d31dee93f4 100644
--- a/nf_core/pipeline-template/README.md
+++ b/nf_core/pipeline-template/README.md
@@ -16,7 +16,7 @@
 [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.10.0-23aa62.svg)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py
index a5b7cf325f..150a89e102 100644
--- a/nf_core/pipelines/lint/nextflow_config.py
+++ b/nf_core/pipelines/lint/nextflow_config.py
@@ -65,14 +65,6 @@ def nextflow_config(self) -> Dict[str, List[str]]:
         * Should always be set to default value:
         ``https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}``
 
-    * ``params.validationShowHiddenParams``
-
-        * Determines whether boilerplate params are showed by schema. Set to ``false`` by default
-
-    * ``params.validationSchemaIgnoreParams``
-
-        * A comma separated string of inputs the schema validation should ignore.
-
     **The following variables throw warnings if missing:**
 
     * ``manifest.mainScript``: The filename of the main pipeline script (should be ``main.nf``)
@@ -151,8 +143,11 @@ def nextflow_config(self) -> Dict[str, List[str]]:
         ["process.time"],
         ["params.outdir"],
         ["params.input"],
-        ["params.validationShowHiddenParams"],
-        ["params.validationSchemaIgnoreParams"],
+        ["validation.help.enabled"],
+        ["validation.help.beforeText"],
+        ["validation.help.afterText"],
+        ["validation.summary.beforeText"],
+        ["validation.summary.afterText"]
     ]
     # Throw a warning if these are missing
     config_warn = [
diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index 9db9457516..78f4317094 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -50,6 +50,7 @@ def __init__(self):
         self.validation_plugin = None
         self.schema_draft = None
         self.defs_notation = None
+        self.ignored_params = []
 
     # Update the validation plugin code everytime the schema gets changed
     def set_schema_filename(self, schema: str) -> None:
@@ -69,16 +70,26 @@ def del_schema_filename(self) -> None:
     def _update_validation_plugin_from_config(self, config: str) -> None:
         plugin = "nf-schema"
         with open(Path(config)) as conf:
-            nf_schema_pattern = re.compile("id\s*[\"']nf-schema", re.MULTILINE)
-            nf_validation_pattern = re.compile("id\s*[\"']nf-validation", re.MULTILINE)
+            nf_schema_pattern = re.compile(r"id\s*[\"']nf-schema", re.MULTILINE)
+            nf_validation_pattern = re.compile(r"id\s*[\"']nf-validation", re.MULTILINE)
             config_content = conf.read()
             if re.search(nf_validation_pattern, config_content):
                 plugin = "nf-validation"
+                self.ignored_params = self.pipeline_params.get("validationSchemaIgnoreParams", "").strip("\"'").split(",")
+                self.ignored_params.append("validationSchemaIgnoreParams")
             elif re.search(nf_schema_pattern, config_content):
                 plugin = "nf-schema"
+                ignored_params_pattern = re.compile(r"defaultIgnoreParams\s*=\s*\[([^\]]*)\]", re.MULTILINE)
+                ignored_params_match = re.search(ignored_params_pattern, config_content)
+                ignored_params = ["help", "helpFull", "showHidden"] # Help parameter should be ignored by default
+                if ignored_params_match and len(ignored_params_match.groups()) == 1:
+                    ignored_params.extend(ignored_params_match.group(1).replace("\"", "").replace("'", '').replace(" ", "").split(","))
+                self.ignored_params = ignored_params
             else:
                 log.warning("Could not find nf-schema or nf-validation in the pipeline config. Defaulting to nf-schema")
             
+
+            
         self.validation_plugin = plugin
         # Previous versions of nf-schema used "defs", but it's advised to use "$defs"
         if plugin == "nf-schema":
@@ -845,13 +856,12 @@ def add_schema_found_configs(self):
         Update defaults if they have changed
         """
         params_added = []
-        params_ignore = self.pipeline_params.get("validationSchemaIgnoreParams", "").strip("\"'").split(",")
-        params_ignore.append("validationSchemaIgnoreParams")
+
         for p_key, p_val in self.pipeline_params.items():
             s_key = self.schema_params.get(p_key)
             # Check if key is in schema parameters
             # Key is in pipeline but not in schema or ignored from schema
-            if p_key not in self.schema_params and p_key not in params_ignore:
+            if p_key not in self.schema_params and p_key not in self.ignored_params:
                 if (
                     self.no_prompts
                     or self.schema_from_scratch
@@ -884,7 +894,7 @@ def add_schema_found_configs(self):
             elif (
                 s_key
                 and (p_key not in self.schema_defaults)
-                and (p_key not in params_ignore)
+                and (p_key not in self.ignored_params)
                 and (p_def := self.build_schema_param(p_val).get("default"))
             ):
                 if self.no_prompts or Confirm.ask(

From af34d0718db98544a8da402952aea87ca778a60e Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 20 Aug 2024 17:50:32 +0200
Subject: [PATCH 19/63] update validation plugin fetching

---
 nf_core/pipeline-template/nextflow.config |  2 +-
 nf_core/pipelines/schema.py               | 58 ++++++++++++-----------
 2 files changed, 32 insertions(+), 28 deletions(-)

diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index ef067dcfab..3a98c40f0a 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -61,7 +61,7 @@ params {
     max_time                   = '240.h'
 
     // Schema validation default options
-    validate_params                  = true
+    validate_params            = true
 
 }
 
diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index 78f4317094..e9c5556dbb 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -69,35 +69,45 @@ def del_schema_filename(self) -> None:
 
     def _update_validation_plugin_from_config(self, config: str) -> None:
         plugin = "nf-schema"
-        with open(Path(config)) as conf:
-            nf_schema_pattern = re.compile(r"id\s*[\"']nf-schema", re.MULTILINE)
-            nf_validation_pattern = re.compile(r"id\s*[\"']nf-validation", re.MULTILINE)
-            config_content = conf.read()
-            if re.search(nf_validation_pattern, config_content):
-                plugin = "nf-validation"
-                self.ignored_params = self.pipeline_params.get("validationSchemaIgnoreParams", "").strip("\"'").split(",")
-                self.ignored_params.append("validationSchemaIgnoreParams")
-            elif re.search(nf_schema_pattern, config_content):
+        conf = nf_core.utils.fetch_wf_config(Path(self.schema_filename).parent)
+
+        plugins = str(conf.get("plugins", "")).strip("\"").strip("'").strip(" ").split(",")
+        plugin_found = False
+        for plugin_instance in plugins:
+            if "nf-schema" in plugin_instance:
                 plugin = "nf-schema"
-                ignored_params_pattern = re.compile(r"defaultIgnoreParams\s*=\s*\[([^\]]*)\]", re.MULTILINE)
-                ignored_params_match = re.search(ignored_params_pattern, config_content)
-                ignored_params = ["help", "helpFull", "showHidden"] # Help parameter should be ignored by default
-                if ignored_params_match and len(ignored_params_match.groups()) == 1:
-                    ignored_params.extend(ignored_params_match.group(1).replace("\"", "").replace("'", '').replace(" ", "").split(","))
-                self.ignored_params = ignored_params
-            else:
-                log.warning("Could not find nf-schema or nf-validation in the pipeline config. Defaulting to nf-schema")
-            
+                plugin_found = True
+                break
+            elif "nf-validation" in plugin_instance:
+                plugin = "nf-validation"
+                plugin_found = True
+                break
+
+        if not plugin_found:
+            log.warning("Could not find nf-schema or nf-validation in the pipeline config. Defaulting to nf-schema")
+
+        if "nf-validation" in plugins:
+            plugin = "nf-validation"
+        elif "nf-schema" in plugins:
+            plugin = "nf-schema"
 
-            
         self.validation_plugin = plugin
         # Previous versions of nf-schema used "defs", but it's advised to use "$defs"
         if plugin == "nf-schema":
             self.defs_notation = "$defs"
+            ignored_params = ["help", "helpFull", "showHidden"] # Help parameter should be ignored by default
+            ignored_params_config = conf.get("validation", {}).get("defaultIgnoreParams", [])
+            if len(ignored_params_config) > 0:
+                ignored_params.extend(ignored_params_config)
+            self.ignored_params = ignored_params
             self.schema_draft = "https://json-schema.org/draft/2020-12/schema"
+
         else:
             self.defs_notation = "definitions"
             self.schema_draft = "https://json-schema.org/draft-07/schema"
+            self.get_wf_params()
+            self.ignored_params = self.pipeline_params.get("validationSchemaIgnoreParams", "").strip("\"'").split(",")
+            self.ignored_params.append("validationSchemaIgnoreParams")
 
     def get_schema_path(
         self, path: Union[str, Path], local_only: bool = False, revision: Union[str, None] = None
@@ -325,17 +335,11 @@ def validate_default_params(self):
         if self.pipeline_params == {}:
             self.get_wf_params()
 
-        # Collect parameters to ignore
-        if "validationSchemaIgnoreParams" in self.pipeline_params:
-            params_ignore = self.pipeline_params.get("validationSchemaIgnoreParams", "").strip("\"'").split(",")
-        else:
-            params_ignore = []
-
         # Go over group keys
         for group_key, group in schema_no_required.get(self.defs_notation, {}).items():
             group_properties = group.get("properties")
             for param in group_properties:
-                if param in params_ignore:
+                if param in self.ignored_params:
                     continue
                 if param in self.pipeline_params:
                     self.validate_config_default_parameter(param, group_properties[param], self.pipeline_params[param])
@@ -348,7 +352,7 @@ def validate_default_params(self):
         ungrouped_properties = self.schema.get("properties")
         if ungrouped_properties:
             for param in ungrouped_properties:
-                if param in params_ignore:
+                if param in self.ignored_params:
                     continue
                 if param in self.pipeline_params:
                     self.validate_config_default_parameter(

From e6381b71c67fcc1ecb18c8b3c6e796dd6df0dec7 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 21 Aug 2024 10:59:31 +0200
Subject: [PATCH 20/63] update plugin linting

---
 nf_core/pipelines/lint/nextflow_config.py | 56 ++++++++---------------
 1 file changed, 20 insertions(+), 36 deletions(-)

diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py
index 150a89e102..bd2f4f768b 100644
--- a/nf_core/pipelines/lint/nextflow_config.py
+++ b/nf_core/pipelines/lint/nextflow_config.py
@@ -1,3 +1,4 @@
+import ast
 import logging
 import re
 from pathlib import Path
@@ -330,6 +331,25 @@ def nextflow_config(self) -> Dict[str, List[str]]:
                 )
             )
 
+    # Lint for plugins
+    config_plugins = ast.literal_eval(self.nf_config.get("plugins", "").strip("\""))
+    found_plugins = []
+    if len(config_plugins) == 0:
+        failed.append("nextflow.config contains an empty plugins scope")
+    for plugin in config_plugins:
+        if "@" not in plugin:
+            failed.append(f"Plugin '{plugin}' does not have a pinned version")
+        found_plugins.append(plugin.split("@")[0])
+
+    if "nf-validation" in found_plugins and "nf-schema" in found_plugins:
+        failed.append("nextflow.config contains both nf-validation and nf-schema")
+    if "nf-validation" not in found_plugins and "nf-schema" not in found_plugins:
+        failed.append("nextflow.config does not contain `nf-validation` or `nf-schema` in the plugins scope")
+
+    if "nf-validation" in found_plugins:
+        warned.append("nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/")
+
+
     # Check for the availability of the "test" configuration profile by parsing nextflow.config
     # Also check for the presence of nf-validation/nf-schema and check if they have pinned versions
     with open(Path(self.wf_path, "nextflow.config")) as f:
@@ -359,42 +379,6 @@ def nextflow_config(self) -> Dict[str, List[str]]:
             else:
                 failed.append("nextflow.config does not contain configuration profile `test`")
 
-        # Lint for nf-validation and nf-schema
-        match_plugins = re.search(r"\bplugins\s*\{([^}]+)}", cleaned_content, re.MULTILINE)
-        if not match_plugins:
-            failed.append(
-                "nextflow.config does not contain `plugins` scope, but `nf-validation` or `nf-schema` plugins are required"
-            )
-        else:
-            found_plugins = {}
-            for line in match_plugins.group(1).split("\n"):
-                cleaned_line = line.split("//")[0].strip().replace("\"", "'")
-                if "id" not in line: continue
-                match_line = re.search(r"\bid\s'([^']+)'", cleaned_line)
-                if not match_line:
-                    failed.append(f"nextflow.config contains an invalid plugins identifier: {cleaned_line}")
-                    continue
-                plugin = match_line.group(1)
-                name = plugin.split("@")[0]
-                version = ""
-                if "@" in plugin:
-                    version = plugin.split("@")[1]
-                found_plugins[name] = version
-
-            if len(found_plugins) == 0:
-                failed.append("nextflow.config contains an empty plugins scope")
-            elif "nf-validation" in found_plugins and "nf-schema" in found_plugins:
-                failed.append("nextflow.config contains both nf-validation and nf-schema")
-            elif "nf-validation" in found_plugins and found_plugins["nf-validation"] == "":
-                failed.append("nextflow.config contains an unpinned version of nf-validation")
-            elif "nf-schema" in found_plugins and found_plugins["nf-schema"] == "":
-                failed.append("nextflow.config contains an unpinned version of nf-schema")
-            elif "nf-validation" not in found_plugins and "nf-schema" not in found_plugins:
-                failed.append("nextflow.config does not contain `nf-validation` or `nf-schema` in the plugins scope")
-
-            if "nf-validation" in found_plugins:
-                warned.append("nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/")
-
     # Check that the default values in nextflow.config match the default values defined in the nextflow_schema.json
     ignore_defaults = []
     for item in ignore_configs:

From e66a732e7db6452fb12b0f311762b19bbe7f3418 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 21 Aug 2024 11:01:16 +0200
Subject: [PATCH 21/63] ignore genomes for now

---
 nf_core/pipeline-template/nextflow.config      | 2 +-
 nf_core/pipeline-template/nextflow_schema.json | 6 ------
 2 files changed, 1 insertion(+), 7 deletions(-)

diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 3a98c40f0a..bb55678001 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -266,7 +266,7 @@ plugins {
 }
 
 validation {
-    parametersSchema = "${projectDir}/nextflow_schema.json"
+    defaultIgnoreParams = ["genomes"]
     help {
         enabled = true
         command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json
index 14120bbabc..908d310171 100644
--- a/nf_core/pipeline-template/nextflow_schema.json
+++ b/nf_core/pipeline-template/nextflow_schema.json
@@ -81,12 +81,6 @@
                     "fa_icon": "fas fa-ban",
                     "hidden": true,
                     "default": "s3://ngi-igenomes/igenomes/"
-                },
-                "genomes": {
-                    "type": "object",
-                    "description": "An object containing all reference data availabe in igenomes",
-                    "fa_icon": "fas fa-ban",
-                    "hidden": true
                 }
             }
         },

From b6ae8d01dd440558cb3a2af821a04ea8fc89591a Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 21 Aug 2024 12:23:52 +0200
Subject: [PATCH 22/63] improve config linting for validation even more

---
 nf_core/pipelines/lint/nextflow_config.py | 59 ++++++++++++++---------
 1 file changed, 35 insertions(+), 24 deletions(-)

diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py
index bd2f4f768b..6e292deb09 100644
--- a/nf_core/pipelines/lint/nextflow_config.py
+++ b/nf_core/pipelines/lint/nextflow_config.py
@@ -144,11 +144,7 @@ def nextflow_config(self) -> Dict[str, List[str]]:
         ["process.time"],
         ["params.outdir"],
         ["params.input"],
-        ["validation.help.enabled"],
-        ["validation.help.beforeText"],
-        ["validation.help.afterText"],
-        ["validation.summary.beforeText"],
-        ["validation.summary.afterText"]
+        ["validation.help.enabled"]
     ]
     # Throw a warning if these are missing
     config_warn = [
@@ -157,6 +153,11 @@ def nextflow_config(self) -> Dict[str, List[str]]:
         ["trace.file"],
         ["report.file"],
         ["dag.file"],
+        ["validation.help.beforeText"],
+        ["validation.help.afterText"],
+        ["validation.help.command"],
+        ["validation.summary.beforeText"],
+        ["validation.summary.afterText"]
     ]
     # Old depreciated vars - fail if present
     config_fail_ifdefined = [
@@ -168,6 +169,35 @@ def nextflow_config(self) -> Dict[str, List[str]]:
         "params.enable_conda",
     ]
 
+    # Lint for plugins
+    config_plugins = ast.literal_eval(self.nf_config.get("plugins", "").strip("\""))
+    found_plugins = []
+    if len(config_plugins) == 0:
+        failed.append("nextflow.config contains an empty plugins scope")
+    for plugin in config_plugins:
+        if "@" not in plugin:
+            failed.append(f"Plugin '{plugin}' does not have a pinned version")
+        found_plugins.append(plugin.split("@")[0])
+
+    if "nf-validation" in found_plugins and "nf-schema" in found_plugins:
+        failed.append("nextflow.config contains both nf-validation and nf-schema")
+    if "nf-validation" not in found_plugins and "nf-schema" not in found_plugins:
+        failed.append("nextflow.config does not contain `nf-validation` or `nf-schema` in the plugins scope")
+
+    if "nf-schema" in found_plugins:
+        if self.nf_config.get("validation.help.enabled", "false") == "false":
+            failed.append("The help message has not been enabled. Set the `validation.help.enabled` configuration option to `true` to enable help messages")
+        config_fail_ifdefined.extend([
+            "params.validationFailUnrecognisedParams",
+            "params.validationLenientMode",
+            "params.validationSchemaIgnoreParams",
+            "params.validationShowHiddenParams"
+        ])
+
+    if "nf-validation" in found_plugins:
+        warned.append("nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/")
+
+
     # Remove field that should be ignored according to the linting config
     ignore_configs = self.lint_config.get("nextflow_config", []) if self.lint_config is not None else []
 
@@ -331,25 +361,6 @@ def nextflow_config(self) -> Dict[str, List[str]]:
                 )
             )
 
-    # Lint for plugins
-    config_plugins = ast.literal_eval(self.nf_config.get("plugins", "").strip("\""))
-    found_plugins = []
-    if len(config_plugins) == 0:
-        failed.append("nextflow.config contains an empty plugins scope")
-    for plugin in config_plugins:
-        if "@" not in plugin:
-            failed.append(f"Plugin '{plugin}' does not have a pinned version")
-        found_plugins.append(plugin.split("@")[0])
-
-    if "nf-validation" in found_plugins and "nf-schema" in found_plugins:
-        failed.append("nextflow.config contains both nf-validation and nf-schema")
-    if "nf-validation" not in found_plugins and "nf-schema" not in found_plugins:
-        failed.append("nextflow.config does not contain `nf-validation` or `nf-schema` in the plugins scope")
-
-    if "nf-validation" in found_plugins:
-        warned.append("nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/")
-
-
     # Check for the availability of the "test" configuration profile by parsing nextflow.config
     # Also check for the presence of nf-validation/nf-schema and check if they have pinned versions
     with open(Path(self.wf_path, "nextflow.config")) as f:

From 1be17370b30fe34adccb5b698d26145e05522e99 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 21 Aug 2024 14:56:37 +0200
Subject: [PATCH 23/63] check plugin includes in pipeline

---
 nf_core/pipelines/lint/__init__.py        |  3 ++
 nf_core/pipelines/lint/nextflow_config.py |  4 ++-
 nf_core/pipelines/lint/plugin_includes.py | 38 +++++++++++++++++++++++
 3 files changed, 44 insertions(+), 1 deletion(-)
 create mode 100644 nf_core/pipelines/lint/plugin_includes.py

diff --git a/nf_core/pipelines/lint/__init__.py b/nf_core/pipelines/lint/__init__.py
index ed833d3219..219cdd8f5c 100644
--- a/nf_core/pipelines/lint/__init__.py
+++ b/nf_core/pipelines/lint/__init__.py
@@ -45,6 +45,7 @@
 from .nfcore_yml import nfcore_yml
 from .pipeline_name_conventions import pipeline_name_conventions
 from .pipeline_todos import pipeline_todos
+from .plugin_includes import plugin_includes
 from .readme import readme
 from .schema_description import schema_description
 from .schema_lint import schema_lint
@@ -92,6 +93,7 @@ class PipelineLint(nf_core.utils.Pipeline):
     nfcore_yml = nfcore_yml
     pipeline_name_conventions = pipeline_name_conventions
     pipeline_todos = pipeline_todos
+    plugin_includes = plugin_includes
     readme = readme
     schema_description = schema_description
     schema_lint = schema_lint
@@ -135,6 +137,7 @@ def _get_all_lint_tests(release_mode):
             "actions_awsfulltest",
             "readme",
             "pipeline_todos",
+            "plugin_includes",
             "pipeline_name_conventions",
             "template_strings",
             "schema_lint",
diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py
index 6e292deb09..a735c5042b 100644
--- a/nf_core/pipelines/lint/nextflow_config.py
+++ b/nf_core/pipelines/lint/nextflow_config.py
@@ -170,7 +170,7 @@ def nextflow_config(self) -> Dict[str, List[str]]:
     ]
 
     # Lint for plugins
-    config_plugins = ast.literal_eval(self.nf_config.get("plugins", "").strip("\""))
+    config_plugins = ast.literal_eval(self.nf_config.get("plugins", ""))
     found_plugins = []
     if len(config_plugins) == 0:
         failed.append("nextflow.config contains an empty plugins scope")
@@ -185,6 +185,7 @@ def nextflow_config(self) -> Dict[str, List[str]]:
         failed.append("nextflow.config does not contain `nf-validation` or `nf-schema` in the plugins scope")
 
     if "nf-schema" in found_plugins:
+        passed.append("Found nf-schema plugin")
         if self.nf_config.get("validation.help.enabled", "false") == "false":
             failed.append("The help message has not been enabled. Set the `validation.help.enabled` configuration option to `true` to enable help messages")
         config_fail_ifdefined.extend([
@@ -195,6 +196,7 @@ def nextflow_config(self) -> Dict[str, List[str]]:
         ])
 
     if "nf-validation" in found_plugins:
+        passed.append("Found nf-validation plugin")
         warned.append("nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/")
 
 
diff --git a/nf_core/pipelines/lint/plugin_includes.py b/nf_core/pipelines/lint/plugin_includes.py
new file mode 100644
index 0000000000..247c4e493b
--- /dev/null
+++ b/nf_core/pipelines/lint/plugin_includes.py
@@ -0,0 +1,38 @@
+import ast
+import glob
+import logging
+import re
+from typing import Dict, List
+
+log = logging.getLogger(__name__)
+
+
+def plugin_includes(self) -> Dict[str, List[str]]:
+    """Checks the include statements in the all *.nf files for plugin includes
+
+    When nf-schema is used in an nf-core pipeline, the include statements of the plugin
+    functions have to use nf-schema instead of nf-validation and vice versa
+    """
+    config_plugins = [plugin.split("@")[0] for plugin in ast.literal_eval(self.nf_config.get("plugins", ""))]
+    validation_plugin = "nf-validation" if "nf-validation" in config_plugins else "nf-schema"
+
+    passed = []
+    warned = []
+    failed = []
+    ignored = []
+
+    plugin_include_pattern = re.compile(r"^include\s*{[^}]+}\s*from\s*[\"']plugin/([^\"']+)[\"']\s*$", re.MULTILINE)
+    workflow_files = [file for file in glob.glob(f"{self.wf_path}/**/*.nf", recursive=True) if not file.startswith("./modules/")]
+    test_passed = True
+    for file in workflow_files:
+        with open(file, "r") as of:
+            plugin_includes = re.findall(plugin_include_pattern, of.read())
+            for include in plugin_includes:
+                if include not in ["nf-validation", "nf-schema"]: continue
+                if include != validation_plugin:
+                    test_passed = False
+                    failed.append(f"Found a `{include}` plugin import in `{file[2:]}`, but `{validation_plugin}` was used in `nextflow.config`")
+
+    if test_passed: passed.append("No wrong validation plugin imports have been found")
+
+    return {"passed": passed, "warned": warned, "failed": failed, "ignored": ignored}

From 2f1a4428dc73e15aea2fc001bec4df323700035e Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Thu, 22 Aug 2024 14:51:07 +0200
Subject: [PATCH 24/63] make nf-schema optional in the template

---
 .../assets/schema_input.json                  |  2 +-
 nf_core/pipeline-template/main.nf             |  1 -
 nf_core/pipeline-template/modules.json        |  4 +-
 nf_core/pipeline-template/nextflow.config     |  9 ++--
 .../pipeline-template/nextflow_schema.json    |  3 +-
 .../utils_nfcore_pipeline_pipeline/main.nf    | 18 +++++---
 .../nf-core/utils_nfcore_pipeline/main.nf     | 46 +++++++++++++++++++
 .../pipeline-template/workflows/pipeline.nf   |  2 +-
 nf_core/pipelines/create/templatefeatures.yml | 10 ++++
 nf_core/pipelines/lint/nextflow_config.py     | 20 ++++----
 10 files changed, 90 insertions(+), 25 deletions(-)

diff --git a/nf_core/pipeline-template/assets/schema_input.json b/nf_core/pipeline-template/assets/schema_input.json
index e76b95fa99..28a468adaf 100644
--- a/nf_core/pipeline-template/assets/schema_input.json
+++ b/nf_core/pipeline-template/assets/schema_input.json
@@ -1,5 +1,5 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "$id": "https://raw.githubusercontent.com/{{ name }}/master/assets/schema_input.json",
     "title": "{{ name }} pipeline - params.input schema",
     "description": "Schema for the file provided with params.input",
diff --git a/nf_core/pipeline-template/main.nf b/nf_core/pipeline-template/main.nf
index fddfc5489e..f644f52afc 100644
--- a/nf_core/pipeline-template/main.nf
+++ b/nf_core/pipeline-template/main.nf
@@ -76,7 +76,6 @@ workflow {
     //
     PIPELINE_INITIALISATION (
         params.version,
-        params.help,
         params.validate_params,
         params.monochrome_logs,
         args,
diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json
index 1a3b96490d..0a883b60b7 100644
--- a/nf_core/pipeline-template/modules.json
+++ b/nf_core/pipeline-template/modules.json
@@ -29,12 +29,12 @@
                         "branch": "master",
                         "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
                         "installed_by": ["subworkflows"]
-                    },
+                    }{% if nf_schema %},
                     "utils_nfschema_plugin": {
                         "branch": "master",
                         "git_sha": "a3e87febb28bd0461c22a917c5b2c1492053ef85",
                         "installed_by": ["subworkflows"]
-                    }
+                    }{% endif %}
                 }
             }
         }
diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index bb55678001..4acc34e409 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -37,9 +37,9 @@ params {
     plaintext_email              = false
     monochrome_logs              = false
     hook_url                     = null
-    help                         = false
+    {% if nf_schema %}help                         = false
     helpFull                     = false
-    showHidden                   = false
+    showHidden                   = false{% endif %}
     version                      = false
     pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
 
@@ -260,13 +260,14 @@ manifest {
     doi             = ''
 }
 
+{% if nf_schema -%}
 // Nextflow plugins
 plugins {
     id 'nf-schema@2.1.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
 }
 
 validation {
-    defaultIgnoreParams = ["genomes"]
+    defaultIgnoreParams = ["genomes", "helpFull", "showHidden", "help-full", "show-hidden"] // The last 4 parameters are here because of a bug in nf-schema. This will be fixed in a later version
     help {
         enabled = true
         command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
@@ -293,7 +294,7 @@ validation {
         afterText = validation.help.afterText
     }
 }
-
+{% endif -%}
 
 // Load modules.config for DSL2 module specific options
 includeConfig 'conf/modules.config'
diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json
index 908d310171..c729c370bf 100644
--- a/nf_core/pipeline-template/nextflow_schema.json
+++ b/nf_core/pipeline-template/nextflow_schema.json
@@ -40,8 +40,7 @@
                     "type": "string",
                     "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
                     "fa_icon": "fas fa-file-signature"
-                }
-                {% endif %}
+                }{% endif %}
             }
         },
         {%- if igenomes %}
diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
index a994cfd584..1fef6912b3 100644
--- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
@@ -8,17 +8,14 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { UTILS_NFSCHEMA_PLUGIN     } from '../../nf-core/utils_nfschema_plugin'
+{% if nf_schema %}include { UTILS_NFSCHEMA_PLUGIN     } from '../../nf-core/utils_nfschema_plugin'
 include { paramsSummaryMap          } from 'plugin/nf-schema'
-include { samplesheetToList         } from 'plugin/nf-schema'
-include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
+include { samplesheetToList         } from 'plugin/nf-schema'{% endif %}
 include { completionEmail           } from '../../nf-core/utils_nfcore_pipeline'
 include { completionSummary         } from '../../nf-core/utils_nfcore_pipeline'
-include { dashedLine                } from '../../nf-core/utils_nfcore_pipeline'
-include { nfCoreLogo                } from '../../nf-core/utils_nfcore_pipeline'
 include { imNotification            } from '../../nf-core/utils_nfcore_pipeline'
 include { UTILS_NFCORE_PIPELINE     } from '../../nf-core/utils_nfcore_pipeline'
-include { workflowCitation          } from '../../nf-core/utils_nfcore_pipeline'
+include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
 
 /*
 ========================================================================================
@@ -50,12 +47,14 @@ workflow PIPELINE_INITIALISATION {
         workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1
     )
 
+    {% if nf_schema %}
     //
     // Validate parameters and generate parameter summary to stdout
     //
     UTILS_NFSCHEMA_PLUGIN (
         validate_params
     )
+    {% endif %}
 
     //
     // Check config provided to the pipeline
@@ -74,6 +73,7 @@ workflow PIPELINE_INITIALISATION {
     //
     // Create channel from input file provided through params.input
     //
+    {% if nf_schema %}
     Channel
         .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
         .map {
@@ -93,6 +93,12 @@ workflow PIPELINE_INITIALISATION {
                 return [ meta, fastqs.flatten() ]
         }
         .set { ch_samplesheet }
+    {% else %}
+    Channel
+        .fromPath(params.input)
+        .splitCsv(header: true, strip: true)
+        .set { ch_samplesheet }
+    {% endif %}
 
     emit:
     samplesheet = ch_samplesheet
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index a5dcd5f83d..14558c3927 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -61,6 +61,25 @@ def checkProfileProvided(nextflow_cli_args) {
     }
 }
 
+//
+// Citation string for pipeline
+//
+def workflowCitation() {
+    def temp_doi_ref = ""
+    String[] manifest_doi = workflow.manifest.doi.tokenize(",")
+    // Using a loop to handle multiple DOIs
+    // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
+    // Removing ` ` since the manifest.doi is a string and not a proper list
+    for (String doi_ref: manifest_doi) temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
+    return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
+        "* The pipeline\n" +
+        temp_doi_ref + "\n" +
+        "* The nf-core framework\n" +
+        "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
+        "* Software dependencies\n" +
+        "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
+}
+
 //
 // Generate workflow version string
 //
@@ -138,6 +157,33 @@ def paramsSummaryMultiqc(summary_params) {
     return yaml_file_text
 }
 
+//
+// nf-core logo
+//
+def nfCoreLogo(monochrome_logs=true) {
+    Map colors = logColours(monochrome_logs)
+    String.format(
+        """\n
+        ${dashedLine(monochrome_logs)}
+                                                ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset}
+        ${colors.blue}        ___     __   __   __   ___     ${colors.green}/,-._.--~\'${colors.reset}
+        ${colors.blue}  |\\ | |__  __ /  ` /  \\ |__) |__         ${colors.yellow}}  {${colors.reset}
+        ${colors.blue}  | \\| |       \\__, \\__/ |  \\ |___     ${colors.green}\\`-._,-`-,${colors.reset}
+                                                ${colors.green}`._,._,\'${colors.reset}
+        ${colors.purple}  ${workflow.manifest.name} ${getWorkflowVersion()}${colors.reset}
+        ${dashedLine(monochrome_logs)}
+        """.stripIndent()
+    )
+}
+
+//
+// Return dashed line
+//
+def dashedLine(monochrome_logs=true) {
+    Map colors = logColours(monochrome_logs)
+    return "-${colors.dim}----------------------------------------------------${colors.reset}-"
+}
+
 //
 // ANSII colours used for terminal logging
 //
diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf
index 4bb0913211..8d2773820d 100644
--- a/nf_core/pipeline-template/workflows/pipeline.nf
+++ b/nf_core/pipeline-template/workflows/pipeline.nf
@@ -6,7 +6,7 @@
 
 include { FASTQC                 } from '../modules/nf-core/fastqc/main'
 {% if multiqc %}include { MULTIQC                } from '../modules/nf-core/multiqc/main'{% endif %}
-include { paramsSummaryMap       } from 'plugin/nf-schema'
+{% if nf_schema %}include { paramsSummaryMap       } from 'plugin/nf-schema'{% endif %}
 {% if multiqc %}include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pipeline'{% endif %}
 include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 {% if citations or multiqc %}include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'{% endif %}
diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml
index b97bf347ab..7a24b3d91a 100644
--- a/nf_core/pipelines/create/templatefeatures.yml
+++ b/nf_core/pipelines/create/templatefeatures.yml
@@ -242,3 +242,13 @@ changelog:
       - "CHANGELOG.md"
   nfcore_pipelines: False
   custom_pipelines: True
+nf_schema:
+  skippable_paths:
+    - "subworkflows/nf-core/utils_nfschema_plugin"
+  short_description: "Use nf-schema for this pipeline."
+  help_text: |
+    nf-schema is used to validate input parameters based on a JSON schema.
+    It also provides helper functionality to create help messages, get a summary
+    of changed parameters and validate and convert a samplesheet to a channel.
+  nfcore_pipelines: False
+  custom_pipelines: False
diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py
index a735c5042b..1dfdabaf10 100644
--- a/nf_core/pipelines/lint/nextflow_config.py
+++ b/nf_core/pipelines/lint/nextflow_config.py
@@ -143,8 +143,7 @@ def nextflow_config(self) -> Dict[str, List[str]]:
         ["process.memory"],
         ["process.time"],
         ["params.outdir"],
-        ["params.input"],
-        ["validation.help.enabled"]
+        ["params.input"]
     ]
     # Throw a warning if these are missing
     config_warn = [
@@ -152,12 +151,7 @@ def nextflow_config(self) -> Dict[str, List[str]]:
         ["timeline.file"],
         ["trace.file"],
         ["report.file"],
-        ["dag.file"],
-        ["validation.help.beforeText"],
-        ["validation.help.afterText"],
-        ["validation.help.command"],
-        ["validation.summary.beforeText"],
-        ["validation.summary.afterText"]
+        ["dag.file"]
     ]
     # Old depreciated vars - fail if present
     config_fail_ifdefined = [
@@ -188,6 +182,16 @@ def nextflow_config(self) -> Dict[str, List[str]]:
         passed.append("Found nf-schema plugin")
         if self.nf_config.get("validation.help.enabled", "false") == "false":
             failed.append("The help message has not been enabled. Set the `validation.help.enabled` configuration option to `true` to enable help messages")
+        config_fail.extend([
+            ["validation.help.enabled"]
+        ])
+        config_warn.extend([
+            ["validation.help.beforeText"],
+            ["validation.help.afterText"],
+            ["validation.help.command"],
+            ["validation.summary.beforeText"],
+            ["validation.summary.afterText"]
+        ])
         config_fail_ifdefined.extend([
             "params.validationFailUnrecognisedParams",
             "params.validationLenientMode",

From 364b54bde2994927d3124bfdf53d97bd1ecc6350 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Thu, 22 Aug 2024 15:57:29 +0200
Subject: [PATCH 25/63] small fixes for template without nf-schema

---
 .../utils_nfcore_pipeline_pipeline/main.nf    | 33 ++++++++++---------
 .../pipeline-template/workflows/pipeline.nf   |  6 ++--
 nf_core/pipelines/lint/nextflow_config.py     |  6 ++--
 nf_core/pipelines/lint/plugin_includes.py     |  2 +-
 4 files changed, 25 insertions(+), 22 deletions(-)

diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
index d96f203544..0867a0a4c9 100644
--- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
@@ -77,9 +77,14 @@ workflow PIPELINE_INITIALISATION {
     //
     // Create channel from input file provided through params.input
     //
-    {% if nf_schema %}
-    Channel
-        .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
+
+    Channel{% if nf_schema %}
+        .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")){% else %}
+        .fromPath(params.input)
+        .splitCsv(header: true, strip: true)
+        .map { row ->
+            [[id:row.sample], row.fastq_1, row.fastq_2]
+        }{% endif %}
         .map {
             meta, fastq_1, fastq_2 ->
                 if (!fastq_2) {
@@ -97,12 +102,6 @@ workflow PIPELINE_INITIALISATION {
                 return [ meta, fastqs.flatten() ]
         }
         .set { ch_samplesheet }
-    {% else %}
-    Channel
-        .fromPath(params.input)
-        .splitCsv(header: true, strip: true)
-        .set { ch_samplesheet }
-    {% endif %}
 
     emit:
     samplesheet = ch_samplesheet
@@ -130,19 +129,21 @@ workflow PIPELINE_COMPLETION {
 
     main:
 
-    summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
-
     //
     // Completion email and summary
     //
     workflow.onComplete {
         {%- if email %}
         if (email || email_on_fail) {
-            {%- if multiqc %}
-            completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, multiqc_report.toList())
-            {%- else %}
-            completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, [])
-            {%- endif %}
+            completionEmail(
+                {% if nf_schema %}paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json"){% else %}{}{% endif %},
+                email,
+                email_on_fail,
+                plaintext_email,
+                outdir,
+                monochrome_logs,
+                {% if multiqc %}multiqc_report.toList(){% else %}[]{% endif %}
+            )
         }
         {%- endif %}
 
diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf
index 8d2773820d..ca5de36a61 100644
--- a/nf_core/pipeline-template/workflows/pipeline.nf
+++ b/nf_core/pipeline-template/workflows/pipeline.nf
@@ -60,9 +60,13 @@ workflow {{ short_name|upper }} {
         Channel.fromPath(params.multiqc_logo, checkIfExists: true) :
         Channel.empty()
 
+    {% if nf_schema %}
     summary_params      = paramsSummaryMap(
         workflow, parameters_schema: "nextflow_schema.json")
     ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
+    ch_multiqc_files = ch_multiqc_files.mix(
+        ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
+    {% endif %}
 
     {%- if citations %}
     ch_multiqc_custom_methods_description = params.multiqc_methods_description ?
@@ -72,8 +76,6 @@ workflow {{ short_name|upper }} {
         methodsDescriptionText(ch_multiqc_custom_methods_description))
     {%- endif %}
 
-    ch_multiqc_files = ch_multiqc_files.mix(
-        ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
     ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)
     {%- if citations %}
     ch_multiqc_files = ch_multiqc_files.mix(
diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py
index 1dfdabaf10..f5689813a4 100644
--- a/nf_core/pipelines/lint/nextflow_config.py
+++ b/nf_core/pipelines/lint/nextflow_config.py
@@ -164,10 +164,10 @@ def nextflow_config(self) -> Dict[str, List[str]]:
     ]
 
     # Lint for plugins
-    config_plugins = ast.literal_eval(self.nf_config.get("plugins", ""))
+    config_plugins = ast.literal_eval(self.nf_config.get("plugins", "[]"))
     found_plugins = []
     if len(config_plugins) == 0:
-        failed.append("nextflow.config contains an empty plugins scope")
+        warned.append("nextflow.config contains an empty plugins scope")
     for plugin in config_plugins:
         if "@" not in plugin:
             failed.append(f"Plugin '{plugin}' does not have a pinned version")
@@ -176,7 +176,7 @@ def nextflow_config(self) -> Dict[str, List[str]]:
     if "nf-validation" in found_plugins and "nf-schema" in found_plugins:
         failed.append("nextflow.config contains both nf-validation and nf-schema")
     if "nf-validation" not in found_plugins and "nf-schema" not in found_plugins:
-        failed.append("nextflow.config does not contain `nf-validation` or `nf-schema` in the plugins scope")
+        warned.append("nextflow.config does not contain `nf-validation` or `nf-schema` in the plugins scope")
 
     if "nf-schema" in found_plugins:
         passed.append("Found nf-schema plugin")
diff --git a/nf_core/pipelines/lint/plugin_includes.py b/nf_core/pipelines/lint/plugin_includes.py
index 247c4e493b..740c001a11 100644
--- a/nf_core/pipelines/lint/plugin_includes.py
+++ b/nf_core/pipelines/lint/plugin_includes.py
@@ -13,7 +13,7 @@ def plugin_includes(self) -> Dict[str, List[str]]:
     When nf-schema is used in an nf-core pipeline, the include statements of the plugin
     functions have to use nf-schema instead of nf-validation and vice versa
     """
-    config_plugins = [plugin.split("@")[0] for plugin in ast.literal_eval(self.nf_config.get("plugins", ""))]
+    config_plugins = [plugin.split("@")[0] for plugin in ast.literal_eval(self.nf_config.get("plugins", "[]"))]
     validation_plugin = "nf-validation" if "nf-validation" in config_plugins else "nf-schema"
 
     passed = []

From 4e631384906d2c02ab537276f22ea47c3ceb438d Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Thu, 22 Aug 2024 16:02:58 +0200
Subject: [PATCH 26/63] bump nextflow version

---
 .github/workflows/create-lint-wf.yml                            | 2 +-
 .github/workflows/create-test-wf.yml                            | 2 +-
 .../nf-core/utils_nextflow_pipeline/tests/nextflow.config       | 2 +-
 .../nf-core/utils_nfcore_pipeline/tests/nextflow.config         | 2 +-
 nf_core/pipelines/lint/readme.py                                | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
index 7e90febb74..f07b31e9de 100644
--- a/.github/workflows/create-lint-wf.yml
+++ b/.github/workflows/create-lint-wf.yml
@@ -38,7 +38,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "23.04.0"
+          - "23.10.0"
           - "latest-everything"
     steps:
       - name: go to subdirectory and change nextflow workdir
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index a95a477459..56c6c822a9 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -39,7 +39,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "23.04.0"
+          - "23.10.0"
           - "latest-everything"
     steps:
       - name: go to working directory
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
index d0a926bf6d..0fa4abaf43 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
@@ -3,7 +3,7 @@ manifest {
     author          = """nf-core"""
     homePage        = 'https://127.0.0.1'
     description     = """Dummy pipeline"""
-    nextflowVersion  = '!>=23.04.0'
+    nextflowVersion  = '!>=23.10.0'
     version         = '9.9.9'
     doi             = 'https://doi.org/10.5281/zenodo.5070524'
 }
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config
index d0a926bf6d..0fa4abaf43 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config
@@ -3,7 +3,7 @@ manifest {
     author          = """nf-core"""
     homePage        = 'https://127.0.0.1'
     description     = """Dummy pipeline"""
-    nextflowVersion  = '!>=23.04.0'
+    nextflowVersion  = '!>=23.10.0'
     version         = '9.9.9'
     doi             = 'https://doi.org/10.5281/zenodo.5070524'
 }
diff --git a/nf_core/pipelines/lint/readme.py b/nf_core/pipelines/lint/readme.py
index 4c16243690..1c09104258 100644
--- a/nf_core/pipelines/lint/readme.py
+++ b/nf_core/pipelines/lint/readme.py
@@ -36,7 +36,7 @@ def readme(self):
 
     if "nextflow_badge" not in ignore_configs:
         # Check that there is a readme badge showing the minimum required version of Nextflow
-        # [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
+        # [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.10.0-23aa62.svg)](https://www.nextflow.io/)
         # and that it has the correct version
         nf_badge_re = r"\[!\[Nextflow\]\(https://img\.shields\.io/badge/nextflow%20DSL2-!?(?:%E2%89%A5|%3E%3D)([\d\.]+)-23aa62\.svg\)\]\(https://www\.nextflow\.io/\)"
         match = re.search(nf_badge_re, content)

From 11efc5547be76f1a6412d049dbfcd10cd337c660 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Thu, 22 Aug 2024 16:08:41 +0200
Subject: [PATCH 27/63] update changelog

---
 CHANGELOG.md | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 98fb925338..b4fcfe8646 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -19,6 +19,8 @@
 - add templatefeatures.yml to python package ([#3112](https://github.com/nf-core/tools/pull/3112))
 - add option to exclude license from pipeline template ([#3125](https://github.com/nf-core/tools/pull/3125))
 - add option to exclude email from pipeline template ([#3126](https://github.com/nf-core/tools/pull/3126))
+- Use nf-schema instead of nf-validation ([#3116](https://github.com/nf-core/tools/pull/3116))
+- add option to exclude nf-schema from the template ([#3116](https://github.com/nf-core/tools/pull/3116))
 
 ### Linting
 
@@ -26,6 +28,10 @@
 - Conda module linting: Include package name in log file ([#3014](https://github.com/nf-core/tools/pull/3014))
 - Restructure pipeline tests and move pipeline linting into subfolder ([#3070](https://github.com/nf-core/tools/pull/3070))
 - Fix module linting warning for process_high_memory ([#3086](https://github.com/nf-core/tools/issues/3086))
+- Linting will now fail when an unpinned plugin is used ([#3116](https://github.com/nf-core/tools/pull/3116))
+- Linting will now check if the schema is correct for the used validation plugin ([#3116])(https://github.com/nf-core/tools/pull/3116)
+- Linting will now check the use of the right validation plugin include statements in the workflow scripts ([#3116])(https://github.com/nf-core/tools/pull/3116)
+- Full linting for correct use of nf-schema and nf-validation ([#3116](https://github.com/nf-core/tools/pull/3116))
 
 ### Download
 

From 47c3fe324280a54d4cae4227ab7679ac488b1edb Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Thu, 22 Aug 2024 16:13:04 +0200
Subject: [PATCH 28/63] fix ruff linting

---
 nf_core/pipelines/lint/nextflow_config.py | 53 +++++++++++------------
 nf_core/pipelines/lint/plugin_includes.py | 24 ++++++----
 nf_core/pipelines/schema.py               | 17 +++++---
 3 files changed, 51 insertions(+), 43 deletions(-)

diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py
index f5689813a4..255042ce5a 100644
--- a/nf_core/pipelines/lint/nextflow_config.py
+++ b/nf_core/pipelines/lint/nextflow_config.py
@@ -143,16 +143,10 @@ def nextflow_config(self) -> Dict[str, List[str]]:
         ["process.memory"],
         ["process.time"],
         ["params.outdir"],
-        ["params.input"]
+        ["params.input"],
     ]
     # Throw a warning if these are missing
-    config_warn = [
-        ["manifest.mainScript"],
-        ["timeline.file"],
-        ["trace.file"],
-        ["report.file"],
-        ["dag.file"]
-    ]
+    config_warn = [["manifest.mainScript"], ["timeline.file"], ["trace.file"], ["report.file"], ["dag.file"]]
     # Old depreciated vars - fail if present
     config_fail_ifdefined = [
         "params.nf_required_version",
@@ -181,28 +175,33 @@ def nextflow_config(self) -> Dict[str, List[str]]:
     if "nf-schema" in found_plugins:
         passed.append("Found nf-schema plugin")
         if self.nf_config.get("validation.help.enabled", "false") == "false":
-            failed.append("The help message has not been enabled. Set the `validation.help.enabled` configuration option to `true` to enable help messages")
-        config_fail.extend([
-            ["validation.help.enabled"]
-        ])
-        config_warn.extend([
-            ["validation.help.beforeText"],
-            ["validation.help.afterText"],
-            ["validation.help.command"],
-            ["validation.summary.beforeText"],
-            ["validation.summary.afterText"]
-        ])
-        config_fail_ifdefined.extend([
-            "params.validationFailUnrecognisedParams",
-            "params.validationLenientMode",
-            "params.validationSchemaIgnoreParams",
-            "params.validationShowHiddenParams"
-        ])
+            failed.append(
+                "The help message has not been enabled. Set the `validation.help.enabled` configuration option to `true` to enable help messages"
+            )
+        config_fail.extend([["validation.help.enabled"]])
+        config_warn.extend(
+            [
+                ["validation.help.beforeText"],
+                ["validation.help.afterText"],
+                ["validation.help.command"],
+                ["validation.summary.beforeText"],
+                ["validation.summary.afterText"],
+            ]
+        )
+        config_fail_ifdefined.extend(
+            [
+                "params.validationFailUnrecognisedParams",
+                "params.validationLenientMode",
+                "params.validationSchemaIgnoreParams",
+                "params.validationShowHiddenParams",
+            ]
+        )
 
     if "nf-validation" in found_plugins:
         passed.append("Found nf-validation plugin")
-        warned.append("nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/")
-
+        warned.append(
+            "nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/"
+        )
 
     # Remove field that should be ignored according to the linting config
     ignore_configs = self.lint_config.get("nextflow_config", []) if self.lint_config is not None else []
diff --git a/nf_core/pipelines/lint/plugin_includes.py b/nf_core/pipelines/lint/plugin_includes.py
index 740c001a11..6a57b1d280 100644
--- a/nf_core/pipelines/lint/plugin_includes.py
+++ b/nf_core/pipelines/lint/plugin_includes.py
@@ -16,23 +16,29 @@ def plugin_includes(self) -> Dict[str, List[str]]:
     config_plugins = [plugin.split("@")[0] for plugin in ast.literal_eval(self.nf_config.get("plugins", "[]"))]
     validation_plugin = "nf-validation" if "nf-validation" in config_plugins else "nf-schema"
 
-    passed = []
-    warned = []
-    failed = []
-    ignored = []
+    passed: list[str] = []
+    warned: list[str] = []
+    failed: list[str] = []
+    ignored: list[str] = []
 
     plugin_include_pattern = re.compile(r"^include\s*{[^}]+}\s*from\s*[\"']plugin/([^\"']+)[\"']\s*$", re.MULTILINE)
-    workflow_files = [file for file in glob.glob(f"{self.wf_path}/**/*.nf", recursive=True) if not file.startswith("./modules/")]
+    workflow_files = [
+        file for file in glob.glob(f"{self.wf_path}/**/*.nf", recursive=True) if not file.startswith("./modules/")
+    ]
     test_passed = True
     for file in workflow_files:
-        with open(file, "r") as of:
+        with open(file) as of:
             plugin_includes = re.findall(plugin_include_pattern, of.read())
             for include in plugin_includes:
-                if include not in ["nf-validation", "nf-schema"]: continue
+                if include not in ["nf-validation", "nf-schema"]:
+                    continue
                 if include != validation_plugin:
                     test_passed = False
-                    failed.append(f"Found a `{include}` plugin import in `{file[2:]}`, but `{validation_plugin}` was used in `nextflow.config`")
+                    failed.append(
+                        f"Found a `{include}` plugin import in `{file[2:]}`, but `{validation_plugin}` was used in `nextflow.config`"
+                    )
 
-    if test_passed: passed.append("No wrong validation plugin imports have been found")
+    if test_passed:
+        passed.append("No wrong validation plugin imports have been found")
 
     return {"passed": passed, "warned": warned, "failed": failed, "ignored": ignored}
diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index e9c5556dbb..ccbc86645e 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -5,7 +5,6 @@
 import logging
 import tempfile
 import webbrowser
-import re
 from pathlib import Path
 from typing import Union
 
@@ -58,10 +57,10 @@ def set_schema_filename(self, schema: str) -> None:
         basepath = "/".join(str(schema).split("/")[:-1])
         config = f"{basepath}/nextflow.config" if basepath != "" else "nextflow.config"
         self._update_validation_plugin_from_config(config)
-    
+
     def get_schema_filename(self) -> str:
         return self._schema_filename
-    
+
     def del_schema_filename(self) -> None:
         del self._schema_filename
 
@@ -71,7 +70,7 @@ def _update_validation_plugin_from_config(self, config: str) -> None:
         plugin = "nf-schema"
         conf = nf_core.utils.fetch_wf_config(Path(self.schema_filename).parent)
 
-        plugins = str(conf.get("plugins", "")).strip("\"").strip("'").strip(" ").split(",")
+        plugins = str(conf.get("plugins", "")).strip('"').strip("'").strip(" ").split(",")
         plugin_found = False
         for plugin_instance in plugins:
             if "nf-schema" in plugin_instance:
@@ -95,7 +94,7 @@ def _update_validation_plugin_from_config(self, config: str) -> None:
         # Previous versions of nf-schema used "defs", but it's advised to use "$defs"
         if plugin == "nf-schema":
             self.defs_notation = "$defs"
-            ignored_params = ["help", "helpFull", "showHidden"] # Help parameter should be ignored by default
+            ignored_params = ["help", "helpFull", "showHidden"]  # Help parameter should be ignored by default
             ignored_params_config = conf.get("validation", {}).get("defaultIgnoreParams", [])
             if len(ignored_params_config) > 0:
                 ignored_params.extend(ignored_params_config)
@@ -447,7 +446,9 @@ def validate_schema(self, schema=None):
 
         # Add a small check for older nf-schema JSON schemas
         if "defs" in schema:
-            raise AssertionError(f'Using "defs" for schema definitions is not supported. Please use {self.defs_notation} instead')
+            raise AssertionError(
+                f'Using "defs" for schema definitions is not supported. Please use {self.defs_notation} instead'
+            )
 
         for d_key, d_schema in schema.get(self.defs_notation, {}).items():
             # Check that this definition is mentioned in allOf
@@ -458,7 +459,9 @@ def validate_schema(self, schema=None):
                 if allOf["$ref"] == f"#/{self.defs_notation}/{d_key}":
                     in_allOf = True
             if not in_allOf:
-                raise AssertionError(f"Definition subschema `#/{self.defs_notation}/{d_key}` not included in schema `allOf`")
+                raise AssertionError(
+                    f"Definition subschema `#/{self.defs_notation}/{d_key}` not included in schema `allOf`"
+                )
 
             # TODO add support for nested parameters
             for d_param_id in d_schema.get("properties", {}):

From 09bfca2663275c37173ce8018c858164974479f8 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Thu, 22 Aug 2024 16:29:39 +0200
Subject: [PATCH 29/63] add a plugin includes test

---
 tests/pipelines/lint/test_plugin_includes.py | 23 ++++++++++++++++++++
 1 file changed, 23 insertions(+)
 create mode 100644 tests/pipelines/lint/test_plugin_includes.py

diff --git a/tests/pipelines/lint/test_plugin_includes.py b/tests/pipelines/lint/test_plugin_includes.py
new file mode 100644
index 0000000000..21e6107c14
--- /dev/null
+++ b/tests/pipelines/lint/test_plugin_includes.py
@@ -0,0 +1,23 @@
+import nf_core.pipelines.lint
+
+from ..test_lint import TestLint
+
+class TestLintNextflowConfig(TestLint):
+    def setUp(self) -> None:
+        super().setUp()
+        self.new_pipeline = self._make_pipeline_copy()
+    
+    def test_default_values_match(self):
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        result = lint_obj.plugin_includes()
+        assert len(result["failed"]) == 0
+        assert len(result["warned"]) == 0
+
+    def test_wrong_include(self):
+        test_path = self.new_pipeline / "test.nf"
+        with open(test_path, "w") as of:
+            of.write("include { paramsSummary } from 'plugin/nf-validation'\n")
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        result = lint_obj.plugin_includes()
+        assert len(result["failed"]) == 1
+        assert len(result["warned"]) == 0
\ No newline at end of file

From 44dbbf7a2b095144cb954bb1ed09578776979c92 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Fri, 23 Aug 2024 09:50:51 +0200
Subject: [PATCH 30/63] update review comments

---
 nf_core/pipeline-template/nextflow.config     | 7 ++++---
 nf_core/pipelines/create/templatefeatures.yml | 7 ++++---
 nf_core/pipelines/lint/nextflow_config.py     | 1 -
 nf_core/pipelines/schema.py                   | 2 +-
 4 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index ad800cc55b..3b3183ece1 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -273,6 +273,7 @@ validation {
     help {
         enabled = true
         command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
+        {% if is_nfcore %}
         beforeText = """
 -\033[2m----------------------------------------------------\033[0m-
                                         \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m
@@ -289,12 +290,12 @@ validation {
 
 * Software dependencies
   https://github.com/${manifest.name}/blob/master/CITATIONS.md
-"""
-    }
+"""{% endif %}
+    }{% if is_nfcore %}
     summary {
         beforeText = validation.help.beforeText
         afterText = validation.help.afterText
-    }
+    }[% endif %]
 }
 {% endif -%}
 
diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml
index 29b53eb0a7..224bc38266 100644
--- a/nf_core/pipelines/create/templatefeatures.yml
+++ b/nf_core/pipelines/create/templatefeatures.yml
@@ -245,13 +245,14 @@ changelog:
 nf_schema:
   skippable_paths:
     - "subworkflows/nf-core/utils_nfschema_plugin"
-  short_description: "Use nf-schema for this pipeline."
+  short_description: "Use nf-schema"
+  description: "Use nf-schema for this pipeline."
   help_text: |
     nf-schema is used to validate input parameters based on a JSON schema.
     It also provides helper functionality to create help messages, get a summary
     of changed parameters and validate and convert a samplesheet to a channel.
-  nfcore_pipelines: False
-  custom_pipelines: False
+  nfcore_pipelines: True
+  custom_pipelines: True
 license:
   skippable_paths:
     - "LICENSE"
diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py
index 255042ce5a..71eb6f118f 100644
--- a/nf_core/pipelines/lint/nextflow_config.py
+++ b/nf_core/pipelines/lint/nextflow_config.py
@@ -367,7 +367,6 @@ def nextflow_config(self) -> Dict[str, List[str]]:
             )
 
     # Check for the availability of the "test" configuration profile by parsing nextflow.config
-    # Also check for the presence of nf-validation/nf-schema and check if they have pinned versions
     with open(Path(self.wf_path, "nextflow.config")) as f:
         content = f.read()
 
diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index ccbc86645e..04f5ca2ace 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -447,7 +447,7 @@ def validate_schema(self, schema=None):
         # Add a small check for older nf-schema JSON schemas
         if "defs" in schema:
             raise AssertionError(
-                f'Using "defs" for schema definitions is not supported. Please use {self.defs_notation} instead'
+                f'Using "defs" for schema definitions is not supported. Please use "{self.defs_notation}" instead'
             )
 
         for d_key, d_schema in schema.get(self.defs_notation, {}).items():

From ea51814bc2b1549c14605ba66591e7043bb5e4b3 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Fri, 23 Aug 2024 10:17:15 +0200
Subject: [PATCH 31/63] remove duplicate code

---
 nf_core/pipelines/schema.py | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index 04f5ca2ace..dbe851415f 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -85,11 +85,6 @@ def _update_validation_plugin_from_config(self, config: str) -> None:
         if not plugin_found:
             log.warning("Could not find nf-schema or nf-validation in the pipeline config. Defaulting to nf-schema")
 
-        if "nf-validation" in plugins:
-            plugin = "nf-validation"
-        elif "nf-schema" in plugins:
-            plugin = "nf-schema"
-
         self.validation_plugin = plugin
         # Previous versions of nf-schema used "defs", but it's advised to use "$defs"
         if plugin == "nf-schema":

From b85ea4da6e8287aef01993009cfeac2e2c71b0cd Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Mon, 26 Aug 2024 17:21:14 +0200
Subject: [PATCH 32/63] update nf-schema subwf

---
 nf_core/pipeline-template/modules.json        |  2 +-
 .../utils_nfcore_pipeline_pipeline/main.nf    | 11 ++++++++--
 .../nf-core/utils_nfschema_plugin/main.nf     | 20 ++++++++++++++++---
 3 files changed, 27 insertions(+), 6 deletions(-)

diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json
index 0a883b60b7..666546b6fb 100644
--- a/nf_core/pipeline-template/modules.json
+++ b/nf_core/pipeline-template/modules.json
@@ -32,7 +32,7 @@
                     }{% if nf_schema %},
                     "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "a3e87febb28bd0461c22a917c5b2c1492053ef85",
+                        "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c",
                         "installed_by": ["subworkflows"]
                     }{% endif %}
                 }
diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
index 0867a0a4c9..16f5784683 100644
--- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
@@ -56,7 +56,9 @@ workflow PIPELINE_INITIALISATION {
     // Validate parameters and generate parameter summary to stdout
     //
     UTILS_NFSCHEMA_PLUGIN (
-        validate_params
+        workflow,
+        validate_params,
+        null
     )
     {% endif %}
 
@@ -128,6 +130,11 @@ workflow PIPELINE_COMPLETION {
     {% if multiqc %}multiqc_report  //  string: Path to MultiQC report{% endif %}
 
     main:
+    {% if nf_schema %}
+    summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
+    {% else %}
+    summary_params = [:]
+    {% endif %}
 
     //
     // Completion email and summary
@@ -136,7 +143,7 @@ workflow PIPELINE_COMPLETION {
         {%- if email %}
         if (email || email_on_fail) {
             completionEmail(
-                {% if nf_schema %}paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json"){% else %}{}{% endif %},
+                summary_params,
                 email,
                 email_on_fail,
                 plaintext_email,
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/main.nf
index 5d1dc7c928..4994303ea0 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/main.nf
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/main.nf
@@ -8,7 +8,13 @@ include { validateParameters } from 'plugin/nf-schema'
 workflow UTILS_NFSCHEMA_PLUGIN {
 
     take:
-    validate_params // boolean: validate the parameters
+    input_workflow      // workflow: the workflow object used by nf-schema to get metadata from the workflow
+    validate_params     // boolean:  validate the parameters
+    parameters_schema   // string:   path to the parameters JSON schema.
+                        //           this has to be the same as the schema given to `validation.parametersSchema`
+                        //           when this input is empty it will automatically use the configured schema or
+                        //           "${projectDir}/nextflow_schema.json" as default. This input should not be empty
+                        //           for meta pipelines
 
     main:
 
@@ -16,14 +22,22 @@ workflow UTILS_NFSCHEMA_PLUGIN {
     // Print parameter summary to stdout. This will display the parameters
     // that differ from the default given in the JSON schema
     //
-    log.info paramsSummaryLog(workflow)
+    if(parameters_schema) {
+        log.info paramsSummaryLog(input_workflow, parameters_schema:parameters_schema)
+    } else {
+        log.info paramsSummaryLog(input_workflow)
+    }
 
     //
     // Validate the parameters using nextflow_schema.json or the schema
     // given via the validation.parametersSchema configuration option
     //
     if(validate_params) {
-        validateParameters()
+        if(parameters_schema) {
+            validateParameters(parameters_schema:parameters_schema)
+        } else {
+            validateParameters()
+        }
     }
 
     emit:

From 0fb97db609f912b91b89129d423634b162dc4538 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Mon, 26 Aug 2024 17:27:44 +0200
Subject: [PATCH 33/63] fix some issues

---
 nf_core/pipeline-template/nextflow.config    | 2 +-
 tests/pipelines/lint/test_plugin_includes.py | 5 +++--
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 3c238ee0ce..b4c7f41134 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -297,7 +297,7 @@ validation {
     summary {
         beforeText = validation.help.beforeText
         afterText = validation.help.afterText
-    }[% endif %]
+    }{% endif %}
 }
 {% endif -%}
 
diff --git a/tests/pipelines/lint/test_plugin_includes.py b/tests/pipelines/lint/test_plugin_includes.py
index 21e6107c14..ca14d5456d 100644
--- a/tests/pipelines/lint/test_plugin_includes.py
+++ b/tests/pipelines/lint/test_plugin_includes.py
@@ -2,11 +2,12 @@
 
 from ..test_lint import TestLint
 
+
 class TestLintNextflowConfig(TestLint):
     def setUp(self) -> None:
         super().setUp()
         self.new_pipeline = self._make_pipeline_copy()
-    
+
     def test_default_values_match(self):
         lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
         result = lint_obj.plugin_includes()
@@ -20,4 +21,4 @@ def test_wrong_include(self):
         lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
         result = lint_obj.plugin_includes()
         assert len(result["failed"]) == 1
-        assert len(result["warned"]) == 0
\ No newline at end of file
+        assert len(result["warned"]) == 0

From 7dee4476669957b3b53cd3e77dd7cdbc7b544a1a Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Mon, 26 Aug 2024 17:33:20 +0200
Subject: [PATCH 34/63] fix linting utils_nfschema_plugin

---
 .../nf-core/utils_nfschema_plugin/meta.yml    | 13 ++++
 .../utils_nfschema_plugin/tests/main.nf.test  | 63 +++++++++++++++++--
 2 files changed, 72 insertions(+), 4 deletions(-)

diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/meta.yml b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/meta.yml
index 90b8cb1898..f7d9f02885 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/meta.yml
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/meta.yml
@@ -9,9 +9,22 @@ keywords:
   - summary
 components: []
 input:
+  - input_workflow:
+      type: object
+      description: |
+        The workflow object of the used pipeline.
+        This object contains meta data used to create the params summary log
   - validate_params:
       type: boolean
       description: Validate the parameters and error if invalid.
+  - parameters_schema:
+      type: string
+      description: |
+        Path to the parameters JSON schema.
+        This has to be the same as the schema given to the `validation.parametersSchema` config
+        option. When this input is empty it will automatically use the configured schema or
+        "${projectDir}/nextflow_schema.json" as default. The schema should not be given in this way
+        for meta pipelines.
 output:
   - dummy_emit:
       type: boolean
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
index 703d3a9b86..842dc432af 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
@@ -1,5 +1,3 @@
-// TODO nf-core: Once you have added the required tests, please run the following command to build this file:
-// nf-core subworkflows test utils_nfschema_plugin
 nextflow_workflow {
 
     name "Test Subworkflow UTILS_NFSCHEMA_PLUGIN"
@@ -9,6 +7,7 @@ nextflow_workflow {
     tag "subworkflows"
     tag "subworkflows_nfcore"
     tag "subworkflows/utils_nfschema_plugin"
+    tag "plugin/nf-schema"
 
     config "./nextflow.config"
 
@@ -23,7 +22,9 @@ nextflow_workflow {
             workflow {
                 """
                 validate_params = false
-                input[0] = validate_params
+                input[0] = workflow
+                input[1] = validate_params
+                input[2] = ""
                 """
             }
         }
@@ -47,7 +48,61 @@ nextflow_workflow {
             workflow {
                 """
                 validate_params = true
-                input[0] = validate_params
+                input[0] = workflow
+                input[1] = validate_params
+                input[2] = ""
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.failed },
+                { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } }
+            )
+        }
+    }
+
+    test("Should run nothing - custom schema") {
+
+        when {
+
+            params {
+                test_data   = ''
+            }
+
+            workflow {
+                """
+                validate_params = false
+                input[0] = workflow
+                input[1] = validate_params
+                input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+
+    test("Should validate params - custom schema") {
+
+        when {
+
+            params {
+                test_data   = ''
+                outdir      = 1
+            }
+
+            workflow {
+                """
+                validate_params = true
+                input[0] = workflow
+                input[1] = validate_params
+                input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
                 """
             }
         }

From 6d01b0faf3c1f62dcc22724197bcf599089a8b3b Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Mon, 26 Aug 2024 17:36:32 +0200
Subject: [PATCH 35/63] update utils subwfs

---
 nf_core/pipeline-template/modules.json        |  4 +-
 .../nf-core/utils_nextflow_pipeline/main.nf   | 24 +++++-----
 .../tests/nextflow.config                     |  2 +-
 .../nf-core/utils_nfcore_pipeline/main.nf     | 45 +++++++++----------
 .../tests/nextflow.config                     |  2 +-
 5 files changed, 37 insertions(+), 40 deletions(-)

diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json
index 19df47df2e..ec1cf1d963 100644
--- a/nf_core/pipeline-template/modules.json
+++ b/nf_core/pipeline-template/modules.json
@@ -23,12 +23,12 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "20c03aede5a80ff520a905cea1f8ca121b5bb661",
+                        "git_sha": "2aacc9ef22bfc627b18eca17e9a3bb13c58aab64",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
+                        "git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab",
                         "installed_by": ["subworkflows"]
                     }{% if nf_schema %},
                     "utils_nfschema_plugin": {
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
index e770d91b97..b54fc16c71 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
@@ -2,10 +2,6 @@
 // Subworkflow with functionality that may be useful for any Nextflow pipeline
 //
 
-import org.yaml.snakeyaml.Yaml
-import groovy.json.JsonOutput
-import nextflow.extension.FilesEx
-
 /*
 ========================================================================================
     SUBWORKFLOW DEFINITION
@@ -58,7 +54,7 @@ workflow UTILS_NEXTFLOW_PIPELINE {
 // Generate version string
 //
 def getWorkflowVersion() {
-    String version_string = ""
+    def version_string = "" as String
     if (workflow.manifest.version) {
         def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
         version_string += "${prefix_v}${workflow.manifest.version}"
@@ -79,10 +75,10 @@ def dumpParametersToJSON(outdir) {
     def timestamp  = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
     def filename   = "params_${timestamp}.json"
     def temp_pf    = new File(workflow.launchDir.toString(), ".${filename}")
-    def jsonStr    = JsonOutput.toJson(params)
-    temp_pf.text   = JsonOutput.prettyPrint(jsonStr)
+    def jsonStr    = groovy.json.JsonOutput.toJson(params)
+    temp_pf.text   = groovy.json.JsonOutput.prettyPrint(jsonStr)
 
-    FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json")
+    nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json")
     temp_pf.delete()
 }
 
@@ -90,7 +86,7 @@ def dumpParametersToJSON(outdir) {
 // When running with -profile conda, warn if channels have not been set-up appropriately
 //
 def checkCondaChannels() {
-    Yaml parser = new Yaml()
+    def parser = new org.yaml.snakeyaml.Yaml()
     def channels = []
     try {
         def config = parser.load("conda config --show channels".execute().text)
@@ -102,14 +98,16 @@ def checkCondaChannels() {
 
     // Check that all channels are present
     // This channel list is ordered by required channel priority.
-    def required_channels_in_order = ['conda-forge', 'bioconda']
+    def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults']
     def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean
 
     // Check that they are in the right order
     def channel_priority_violation = false
-    def n = required_channels_in_order.size()
-    for (int i = 0; i < n - 1; i++) {
-        channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1]))
+
+    required_channels_in_order.eachWithIndex { channel, index ->
+        if (index < required_channels_in_order.size() - 1) {
+            channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index+1]))
+        }
     }
 
     if (channels_missing | channel_priority_violation) {
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
index 0fa4abaf43..a09572e5bb 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
@@ -3,7 +3,7 @@ manifest {
     author          = """nf-core"""
     homePage        = 'https://127.0.0.1'
     description     = """Dummy pipeline"""
-    nextflowVersion  = '!>=23.10.0'
+    nextflowVersion = '!>=23.04.0'
     version         = '9.9.9'
     doi             = 'https://doi.org/10.5281/zenodo.5070524'
 }
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index 14558c3927..cbd8495bb6 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -2,9 +2,6 @@
 // Subworkflow with utility functions specific to the nf-core pipeline template
 //
 
-import org.yaml.snakeyaml.Yaml
-import nextflow.extension.FilesEx
-
 /*
 ========================================================================================
     SUBWORKFLOW DEFINITION
@@ -34,7 +31,7 @@ workflow UTILS_NFCORE_PIPELINE {
 //  Warn if a -profile or Nextflow config has not been provided to run the pipeline
 //
 def checkConfigProvided() {
-    valid_config = true
+    def valid_config = true as Boolean
     if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) {
         log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" +
             "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" +
@@ -66,11 +63,13 @@ def checkProfileProvided(nextflow_cli_args) {
 //
 def workflowCitation() {
     def temp_doi_ref = ""
-    String[] manifest_doi = workflow.manifest.doi.tokenize(",")
+    def manifest_doi = workflow.manifest.doi.tokenize(",")
     // Using a loop to handle multiple DOIs
     // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
     // Removing ` ` since the manifest.doi is a string and not a proper list
-    for (String doi_ref: manifest_doi) temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
+    manifest_doi.each { doi_ref ->
+        temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
+    }
     return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
         "* The pipeline\n" +
         temp_doi_ref + "\n" +
@@ -84,7 +83,7 @@ def workflowCitation() {
 // Generate workflow version string
 //
 def getWorkflowVersion() {
-    String version_string = ""
+    def version_string = "" as String
     if (workflow.manifest.version) {
         def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
         version_string += "${prefix_v}${workflow.manifest.version}"
@@ -102,8 +101,8 @@ def getWorkflowVersion() {
 // Get software versions for pipeline
 //
 def processVersionsFromYAML(yaml_file) {
-    Yaml yaml = new Yaml()
-    versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] }
+    def yaml = new org.yaml.snakeyaml.Yaml()
+    def versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] }
     return yaml.dumpAsMap(versions).trim()
 }
 
@@ -124,7 +123,7 @@ def workflowVersionToYAML() {
 def softwareVersionsToYAML(ch_versions) {
     return ch_versions
                 .unique()
-                .map { processVersionsFromYAML(it) }
+                .map { version -> processVersionsFromYAML(version) }
                 .unique()
                 .mix(Channel.of(workflowVersionToYAML()))
 }
@@ -134,19 +133,19 @@ def softwareVersionsToYAML(ch_versions) {
 //
 def paramsSummaryMultiqc(summary_params) {
     def summary_section = ''
-    for (group in summary_params.keySet()) {
+    summary_params.keySet().each { group ->
         def group_params = summary_params.get(group)  // This gets the parameters of that particular group
         if (group_params) {
             summary_section += "    <p style=\"font-size:110%\"><b>$group</b></p>\n"
             summary_section += "    <dl class=\"dl-horizontal\">\n"
-            for (param in group_params.keySet()) {
+            group_params.keySet().sort().each { param ->
                 summary_section += "        <dt>$param</dt><dd><samp>${group_params.get(param) ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>\n"
             }
             summary_section += "    </dl>\n"
         }
     }
 
-    String yaml_file_text  = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n"
+    def yaml_file_text  = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" as String
     yaml_file_text        += "description: ' - this information is collected when the pipeline is started.'\n"
     yaml_file_text        += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
     yaml_file_text        += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
@@ -161,7 +160,7 @@ def paramsSummaryMultiqc(summary_params) {
 // nf-core logo
 //
 def nfCoreLogo(monochrome_logs=true) {
-    Map colors = logColours(monochrome_logs)
+    def colors = logColours(monochrome_logs) as Map
     String.format(
         """\n
         ${dashedLine(monochrome_logs)}
@@ -180,7 +179,7 @@ def nfCoreLogo(monochrome_logs=true) {
 // Return dashed line
 //
 def dashedLine(monochrome_logs=true) {
-    Map colors = logColours(monochrome_logs)
+    def colors = logColours(monochrome_logs) as Map
     return "-${colors.dim}----------------------------------------------------${colors.reset}-"
 }
 
@@ -188,7 +187,7 @@ def dashedLine(monochrome_logs=true) {
 // ANSII colours used for terminal logging
 //
 def logColours(monochrome_logs=true) {
-    Map colorcodes = [:]
+    def colorcodes = [:] as Map
 
     // Reset / Meta
     colorcodes['reset']      = monochrome_logs ? '' : "\033[0m"
@@ -287,7 +286,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     }
 
     def summary = [:]
-    for (group in summary_params.keySet()) {
+    summary_params.keySet().sort().each { group ->
         summary << summary_params[group]
     }
 
@@ -344,10 +343,10 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     def sendmail_html          = sendmail_template.toString()
 
     // Send the HTML e-mail
-    Map colors = logColours(monochrome_logs)
+    def colors = logColours(monochrome_logs) as Map
     if (email_address) {
         try {
-            if (plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
+            if (plaintext_email) { throw new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') }
             // Try to send HTML e-mail using sendmail
             def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html")
             sendmail_tf.withWriter { w -> w << sendmail_html }
@@ -364,13 +363,13 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     // Write summary e-mail HTML to a file
     def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html")
     output_hf.withWriter { w -> w << email_html }
-    FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html");
+    nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html");
     output_hf.delete()
 
     // Write summary e-mail TXT to a file
     def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt")
     output_tf.withWriter { w -> w << email_txt }
-    FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt");
+    nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt");
     output_tf.delete()
 }
 
@@ -378,7 +377,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
 // Print pipeline summary on completion
 //
 def completionSummary(monochrome_logs=true) {
-    Map colors = logColours(monochrome_logs)
+    def colors = logColours(monochrome_logs) as Map
     if (workflow.success) {
         if (workflow.stats.ignoredCount == 0) {
             log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-"
@@ -395,7 +394,7 @@ def completionSummary(monochrome_logs=true) {
 //
 def imNotification(summary_params, hook_url) {
     def summary = [:]
-    for (group in summary_params.keySet()) {
+    summary_params.keySet().sort().each { group ->
         summary << summary_params[group]
     }
 
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config
index 0fa4abaf43..d0a926bf6d 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config
@@ -3,7 +3,7 @@ manifest {
     author          = """nf-core"""
     homePage        = 'https://127.0.0.1'
     description     = """Dummy pipeline"""
-    nextflowVersion  = '!>=23.10.0'
+    nextflowVersion  = '!>=23.04.0'
     version         = '9.9.9'
     doi             = 'https://doi.org/10.5281/zenodo.5070524'
 }

From a7dcdd7b6a02a8cd4a4876a0b888d43de3252f66 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 27 Aug 2024 09:19:09 +0200
Subject: [PATCH 36/63] fix some linting issues

---
 nf_core/pipelines/lint/files_exist.py     |  4 +-
 nf_core/pipelines/lint/nextflow_config.py | 67 +++++++++++------------
 nf_core/pipelines/schema.py               |  2 +-
 3 files changed, 35 insertions(+), 38 deletions(-)

diff --git a/nf_core/pipelines/lint/files_exist.py b/nf_core/pipelines/lint/files_exist.py
index ad0605dcf7..e944882187 100644
--- a/nf_core/pipelines/lint/files_exist.py
+++ b/nf_core/pipelines/lint/files_exist.py
@@ -200,9 +200,7 @@ def files_exist(self) -> Dict[str, List[str]]:
         Path("Singularity"),
     ]
     files_warn_ifexists = [Path(".travis.yml")]
-    files_fail_ifinconfig: List[Tuple[Path, List[Dict[str, str]]]] = [
-        (Path("lib", "nfcore_external_java_deps.jar"), [{"plugins": "nf-validation"}, {"plugins": "nf-schema"}]),
-    ]
+    files_fail_ifinconfig: List[Tuple[Path, List[Dict[str, str]]]] = []
 
     # Remove files that should be ignored according to the linting config
     ignore_files = self.lint_config.get("files_exist", []) if self.lint_config is not None else []
diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py
index 71eb6f118f..2159d7939a 100644
--- a/nf_core/pipelines/lint/nextflow_config.py
+++ b/nf_core/pipelines/lint/nextflow_config.py
@@ -160,48 +160,47 @@ def nextflow_config(self) -> Dict[str, List[str]]:
     # Lint for plugins
     config_plugins = ast.literal_eval(self.nf_config.get("plugins", "[]"))
     found_plugins = []
-    if len(config_plugins) == 0:
-        warned.append("nextflow.config contains an empty plugins scope")
     for plugin in config_plugins:
         if "@" not in plugin:
             failed.append(f"Plugin '{plugin}' does not have a pinned version")
         found_plugins.append(plugin.split("@")[0])
 
-    if "nf-validation" in found_plugins and "nf-schema" in found_plugins:
-        failed.append("nextflow.config contains both nf-validation and nf-schema")
-    if "nf-validation" not in found_plugins and "nf-schema" not in found_plugins:
-        warned.append("nextflow.config does not contain `nf-validation` or `nf-schema` in the plugins scope")
+    if "nf-validation" in found_plugins or "nf-schema" in found_plugins:
+        if "nf-validation" in found_plugins and "nf-schema" in found_plugins:
+            failed.append("nextflow.config contains both nf-validation and nf-schema")
+        if "nf-validation" not in found_plugins and "nf-schema" not in found_plugins:
+            warned.append("nextflow.config does not contain `nf-validation` or `nf-schema` in the plugins scope")
 
-    if "nf-schema" in found_plugins:
-        passed.append("Found nf-schema plugin")
-        if self.nf_config.get("validation.help.enabled", "false") == "false":
-            failed.append(
-                "The help message has not been enabled. Set the `validation.help.enabled` configuration option to `true` to enable help messages"
+        if "nf-schema" in found_plugins:
+            passed.append("Found nf-schema plugin")
+            if self.nf_config.get("validation.help.enabled", "false") == "false":
+                failed.append(
+                    "The help message has not been enabled. Set the `validation.help.enabled` configuration option to `true` to enable help messages"
+                )
+            config_fail.extend([["validation.help.enabled"]])
+            config_warn.extend(
+                [
+                    ["validation.help.beforeText"],
+                    ["validation.help.afterText"],
+                    ["validation.help.command"],
+                    ["validation.summary.beforeText"],
+                    ["validation.summary.afterText"],
+                ]
+            )
+            config_fail_ifdefined.extend(
+                [
+                    "params.validationFailUnrecognisedParams",
+                    "params.validationLenientMode",
+                    "params.validationSchemaIgnoreParams",
+                    "params.validationShowHiddenParams",
+                ]
             )
-        config_fail.extend([["validation.help.enabled"]])
-        config_warn.extend(
-            [
-                ["validation.help.beforeText"],
-                ["validation.help.afterText"],
-                ["validation.help.command"],
-                ["validation.summary.beforeText"],
-                ["validation.summary.afterText"],
-            ]
-        )
-        config_fail_ifdefined.extend(
-            [
-                "params.validationFailUnrecognisedParams",
-                "params.validationLenientMode",
-                "params.validationSchemaIgnoreParams",
-                "params.validationShowHiddenParams",
-            ]
-        )
 
-    if "nf-validation" in found_plugins:
-        passed.append("Found nf-validation plugin")
-        warned.append(
-            "nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/"
-        )
+        if "nf-validation" in found_plugins:
+            passed.append("Found nf-validation plugin")
+            warned.append(
+                "nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/"
+            )
 
     # Remove field that should be ignored according to the linting config
     ignore_configs = self.lint_config.get("nextflow_config", []) if self.lint_config is not None else []
diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index dbe851415f..13b8f62641 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -83,7 +83,7 @@ def _update_validation_plugin_from_config(self, config: str) -> None:
                 break
 
         if not plugin_found:
-            log.warning("Could not find nf-schema or nf-validation in the pipeline config. Defaulting to nf-schema")
+            log.info("Could not find nf-schema or nf-validation in the pipeline config. Defaulting to nf-schema notation for the JSON schema.")
 
         self.validation_plugin = plugin
         # Previous versions of nf-schema used "defs", but it's advised to use "$defs"

From fcdf65be8eef12b7f2c94f7e575c1fbaef8f51da Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 27 Aug 2024 09:21:38 +0200
Subject: [PATCH 37/63] ruff

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

diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index 13b8f62641..76f085a49d 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -83,7 +83,9 @@ def _update_validation_plugin_from_config(self, config: str) -> None:
                 break
 
         if not plugin_found:
-            log.info("Could not find nf-schema or nf-validation in the pipeline config. Defaulting to nf-schema notation for the JSON schema.")
+            log.info(
+                "Could not find nf-schema or nf-validation in the pipeline config. Defaulting to nf-schema notation for the JSON schema."
+            )
 
         self.validation_plugin = plugin
         # Previous versions of nf-schema used "defs", but it's advised to use "$defs"

From 56150dc2e95f0cd99752f263d56a649e5a9822b0 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 27 Aug 2024 09:23:59 +0200
Subject: [PATCH 38/63] add linting doc for plugin_includes

---
 docs/api/_src/pipeline_lint_tests/plugin_includes.md | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100644 docs/api/_src/pipeline_lint_tests/plugin_includes.md

diff --git a/docs/api/_src/pipeline_lint_tests/plugin_includes.md b/docs/api/_src/pipeline_lint_tests/plugin_includes.md
new file mode 100644
index 0000000000..48bddadc80
--- /dev/null
+++ b/docs/api/_src/pipeline_lint_tests/plugin_includes.md
@@ -0,0 +1,5 @@
+# plugin_includes
+
+```{eval-rst}
+.. automethod:: nf_core.pipelines.lint.PipelineLint.plugin_includes
+```

From 5a29c4ef39faefc7f50e30f55c093411adb3f5e0 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 27 Aug 2024 09:38:47 +0200
Subject: [PATCH 39/63] readd file exists check

---
 nf_core/pipelines/lint/files_exist.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/nf_core/pipelines/lint/files_exist.py b/nf_core/pipelines/lint/files_exist.py
index e944882187..7bfbae8ec9 100644
--- a/nf_core/pipelines/lint/files_exist.py
+++ b/nf_core/pipelines/lint/files_exist.py
@@ -198,6 +198,7 @@ def files_exist(self) -> Dict[str, List[str]]:
         Path("parameters.settings.json"),
         Path("pipeline_template.yml"),  # saving information in .nf-core.yml
         Path("Singularity"),
+        Path("lib", "nfcore_external_java_deps.jar"),
     ]
     files_warn_ifexists = [Path(".travis.yml")]
     files_fail_ifinconfig: List[Tuple[Path, List[Dict[str, str]]]] = []

From 18738ef7292891c4f7cd29676af2d4457769822c Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 27 Aug 2024 09:50:58 +0200
Subject: [PATCH 40/63] fix launch command

---
 nf_core/pipelines/launch.py    | 23 ++++++++++++++++-------
 tests/pipelines/test_launch.py | 10 +++++-----
 2 files changed, 21 insertions(+), 12 deletions(-)

diff --git a/nf_core/pipelines/launch.py b/nf_core/pipelines/launch.py
index e03982a25a..a14a8d6d72 100644
--- a/nf_core/pipelines/launch.py
+++ b/nf_core/pipelines/launch.py
@@ -263,15 +263,22 @@ def set_schema_inputs(self):
 
     def merge_nxf_flag_schema(self):
         """Take the Nextflow flag schema and merge it with the pipeline schema"""
+        if "allOf" not in self.schema_obj.schema:
+            self.schema_obj.schema["allOf"] = []
         # Add the coreNextflow subschema to the schema definitions
-        if "definitions" not in self.schema_obj.schema:
+        if "$defs" in self.schema_obj.schema or "definitions" not in self.schema_obj.schema:
+            if "$defs" not in self.schema_obj.schema:
+                self.schema_obj["$defs"] = {}
+            self.schema_obj.schema["$defs"].update(self.nxf_flag_schema)
+            self.schema_obj.schema["allOf"].insert(0, {"$ref": "#/$defs/coreNextflow"})
+
+        if "definitions" in self.schema_obj.schema:
             self.schema_obj.schema["definitions"] = {}
-        self.schema_obj.schema["definitions"].update(self.nxf_flag_schema)
+            self.schema_obj.schema["definitions"].update(self.nxf_flag_schema)
+            self.schema_obj.schema["allOf"].insert(0, {"$ref": "#/definitions/coreNextflow"})
         # Add the new defintion to the allOf key so that it's included in validation
         # Put it at the start of the list so that it comes first
-        if "allOf" not in self.schema_obj.schema:
-            self.schema_obj.schema["allOf"] = []
-        self.schema_obj.schema["allOf"].insert(0, {"$ref": "#/definitions/coreNextflow"})
+
 
     def prompt_web_gui(self):
         """Ask whether to use the web-based or cli wizard to collect params"""
@@ -379,7 +386,8 @@ def sanitise_web_response(self):
         for param_id, param_obj in self.schema_obj.schema.get("properties", {}).items():
             questionary_objects[param_id] = self.single_param_to_questionary(param_id, param_obj, print_help=False)
 
-        for _, definition in self.schema_obj.schema.get("definitions", {}).items():
+        definitions_schemas = self.schema_obj.schema.get("$defs", self.schema_obj.schema.get("definitions", {})).items()
+        for _, definition in definitions_schemas:
             for param_id, param_obj in definition.get("properties", {}).items():
                 questionary_objects[param_id] = self.single_param_to_questionary(param_id, param_obj, print_help=False)
 
@@ -399,9 +407,10 @@ def prompt_schema(self):
         """Go through the pipeline schema and prompt user to change defaults"""
         answers = {}
         # Start with the subschema in the definitions - use order of allOf
+        definitions_schemas = self.schema_obj.schema.get("$defs", self.schema_obj.schema.get("definitions", {})).items()
         for allOf in self.schema_obj.schema.get("allOf", []):
             d_key = allOf["$ref"][14:]
-            answers.update(self.prompt_group(d_key, self.schema_obj.schema["definitions"][d_key]))
+            answers.update(self.prompt_group(d_key, definitions_schemas[d_key]))
 
         # Top level schema params
         for param_id, param_obj in self.schema_obj.schema.get("properties", {}).items():
diff --git a/tests/pipelines/test_launch.py b/tests/pipelines/test_launch.py
index 7c6e3d6196..d63e7b6dc5 100644
--- a/tests/pipelines/test_launch.py
+++ b/tests/pipelines/test_launch.py
@@ -47,7 +47,7 @@ def test_launch_file_exists_overwrite(self, mock_webbrowser, mock_lauch_web_gui,
     def test_get_pipeline_schema(self):
         """Test loading the params schema from a pipeline"""
         self.launcher.get_pipeline_schema()
-        assert len(self.launcher.schema_obj.schema["definitions"]["input_output_options"]["properties"]) > 2
+        assert len(self.launcher.schema_obj.schema["$defs"]["input_output_options"]["properties"]) > 2
 
     @with_temporary_folder
     def test_make_pipeline_schema(self, tmp_path):
@@ -60,8 +60,8 @@ def test_make_pipeline_schema(self, tmp_path):
         Path(test_pipeline_dir, "nextflow_schema.json").unlink()
         self.launcher = nf_core.pipelines.launch.Launch(test_pipeline_dir, params_out=self.nf_params_fn)
         self.launcher.get_pipeline_schema()
-        assert len(self.launcher.schema_obj.schema["definitions"]["input_output_options"]["properties"]) >= 2
-        assert self.launcher.schema_obj.schema["definitions"]["input_output_options"]["properties"]["outdir"] == {
+        assert len(self.launcher.schema_obj.schema["$defs"]["input_output_options"]["properties"]) >= 2
+        assert self.launcher.schema_obj.schema["$defs"]["input_output_options"]["properties"]["outdir"] == {
             "type": "string",
             "format": "directory-path",
             "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
@@ -91,8 +91,8 @@ def test_nf_merge_schema(self):
         self.launcher.get_pipeline_schema()
         self.launcher.set_schema_inputs()
         self.launcher.merge_nxf_flag_schema()
-        assert self.launcher.schema_obj.schema["allOf"][0] == {"$ref": "#/definitions/coreNextflow"}
-        assert "-resume" in self.launcher.schema_obj.schema["definitions"]["coreNextflow"]["properties"]
+        assert self.launcher.schema_obj.schema["allOf"][0] == {"$ref": "#/$defs/coreNextflow"}
+        assert "-resume" in self.launcher.schema_obj.schema["$defs"]["coreNextflow"]["properties"]
 
     def test_ob_to_questionary_string(self):
         """Check converting a python dict to a pyenquirer format - simple strings"""

From ebf6a27c7d9869e19d8bf5c67467bf59cb7d543c Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 27 Aug 2024 10:26:00 +0200
Subject: [PATCH 41/63] fix schema tests

---
 nf_core/pipelines/schema.py    | 13 ++++++-----
 tests/pipelines/test_schema.py | 41 ++++++++++++++++++----------------
 2 files changed, 29 insertions(+), 25 deletions(-)

diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index 76f085a49d..6c1c198bb8 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -54,9 +54,7 @@ def __init__(self):
     # Update the validation plugin code everytime the schema gets changed
     def set_schema_filename(self, schema: str) -> None:
         self._schema_filename = schema
-        basepath = "/".join(str(schema).split("/")[:-1])
-        config = f"{basepath}/nextflow.config" if basepath != "" else "nextflow.config"
-        self._update_validation_plugin_from_config(config)
+        self._update_validation_plugin_from_config()
 
     def get_schema_filename(self) -> str:
         return self._schema_filename
@@ -66,9 +64,12 @@ def del_schema_filename(self) -> None:
 
     schema_filename = property(get_schema_filename, set_schema_filename, del_schema_filename)
 
-    def _update_validation_plugin_from_config(self, config: str) -> None:
+    def _update_validation_plugin_from_config(self) -> None:
         plugin = "nf-schema"
-        conf = nf_core.utils.fetch_wf_config(Path(self.schema_filename).parent)
+        if self.schema_filename:
+            conf = nf_core.utils.fetch_wf_config(Path(self.schema_filename).parent)
+        else:
+            conf = nf_core.utils.fetch_wf_config(Path(self.pipeline_dir))
 
         plugins = str(conf.get("plugins", "")).strip('"').strip("'").strip(" ").split(",")
         plugin_found = False
@@ -464,7 +465,7 @@ def validate_schema(self, schema=None):
             for d_param_id in d_schema.get("properties", {}):
                 # Check that we don't have any duplicate parameter IDs in different definitions
                 if d_param_id in param_keys:
-                    raise AssertionError(f"Duplicate parameter found in schema `definitions`: `{d_param_id}`")
+                    raise AssertionError(f"Duplicate parameter found in schema `{self.defs_notation}`: `{d_param_id}`")
                 param_keys.append(d_param_id)
                 num_params += 1
 
diff --git a/tests/pipelines/test_schema.py b/tests/pipelines/test_schema.py
index 777d959e66..2abaf07bd2 100644
--- a/tests/pipelines/test_schema.py
+++ b/tests/pipelines/test_schema.py
@@ -24,6 +24,9 @@ class TestSchema(unittest.TestCase):
     def setUp(self):
         """Create a new PipelineSchema object"""
         self.schema_obj = nf_core.pipelines.schema.PipelineSchema()
+        self.schema_obj.schema_draft = "https://json-schema.org/draft/2020-12/schema"
+        self.schema_obj.defs_notation = "$defs"
+        self.schema_obj.validation_plugin = "nf-schema"
         self.root_repo_dir = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))
 
         # Create a test pipeline in temp directory
@@ -105,7 +108,7 @@ def test_schema_docs(self):
         docs = self.schema_obj.print_documentation()
         assert self.schema_obj.schema["title"] in docs
         assert self.schema_obj.schema["description"] in docs
-        for definition in self.schema_obj.schema.get("definitions", {}).values():
+        for definition in self.schema_obj.schema.get("$defs", {}).values():
             assert definition["title"] in docs
             assert definition["description"] in docs
 
@@ -175,43 +178,43 @@ def test_validate_schema_fail_duplicate_ids(self):
         Check that the schema validation fails when we have duplicate IDs in definition subschema
         """
         self.schema_obj.schema = {
-            "$schema": "http://json-schema.org/draft-07/schema",
-            "definitions": {"groupOne": {"properties": {"foo": {}}}, "groupTwo": {"properties": {"foo": {}}}},
-            "allOf": [{"$ref": "#/definitions/groupOne"}, {"$ref": "#/definitions/groupTwo"}],
+            "$schema": "https://json-schema.org/draft/2020-12/schema",
+            "$defs": {"groupOne": {"properties": {"foo": {}}}, "groupTwo": {"properties": {"foo": {}}}},
+            "allOf": [{"$ref": "#/$defs/groupOne"}, {"$ref": "#/$defs/groupTwo"}],
         }
         with pytest.raises(AssertionError) as exc_info:
             self.schema_obj.validate_schema(self.schema_obj.schema)
-        assert exc_info.value.args[0] == "Duplicate parameter found in schema `definitions`: `foo`"
+        assert exc_info.value.args[0] == "Duplicate parameter found in schema `$defs`: `foo`"
 
     def test_validate_schema_fail_missing_def(self):
         """
-        Check that the schema validation fails when we a definition in allOf is not in definitions
+        Check that the schema validation fails when we a definition in allOf is not in $defs
         """
         self.schema_obj.schema = {
-            "$schema": "http://json-schema.org/draft-07/schema",
-            "definitions": {"groupOne": {"properties": {"foo": {}}}, "groupTwo": {"properties": {"bar": {}}}},
-            "allOf": [{"$ref": "#/definitions/groupOne"}],
+            "$schema": "https://json-schema.org/draft/2020-12/schema",
+            "$defs": {"groupOne": {"properties": {"foo": {}}}, "groupTwo": {"properties": {"bar": {}}}},
+            "allOf": [{"$ref": "#/$defs/groupOne"}],
         }
         with pytest.raises(AssertionError) as exc_info:
             self.schema_obj.validate_schema(self.schema_obj.schema)
-        assert exc_info.value.args[0] == "Definition subschema `#/definitions/groupTwo` not included in schema `allOf`"
+        assert exc_info.value.args[0] == "Definition subschema `#/$defs/groupTwo` not included in schema `allOf`"
 
     def test_validate_schema_fail_unexpected_allof(self):
         """
         Check that the schema validation fails when we an unrecognised definition is in allOf
         """
         self.schema_obj.schema = {
-            "$schema": "http://json-schema.org/draft-07/schema",
-            "definitions": {"groupOne": {"properties": {"foo": {}}}, "groupTwo": {"properties": {"bar": {}}}},
+            "$schema": "https://json-schema.org/draft/2020-12/schema",
+            "$defs": {"groupOne": {"properties": {"foo": {}}}, "groupTwo": {"properties": {"bar": {}}}},
             "allOf": [
-                {"$ref": "#/definitions/groupOne"},
-                {"$ref": "#/definitions/groupTwo"},
-                {"$ref": "#/definitions/groupThree"},
+                {"$ref": "#/$defs/groupOne"},
+                {"$ref": "#/$defs/groupTwo"},
+                {"$ref": "#/$defs/groupThree"},
             ],
         }
         with pytest.raises(AssertionError) as exc_info:
             self.schema_obj.validate_schema(self.schema_obj.schema)
-        assert exc_info.value.args[0] == "Subschema `groupThree` found in `allOf` but not `definitions`"
+        assert exc_info.value.args[0] == "Subschema `groupThree` found in `allOf` but not `$defs`"
 
     def test_make_skeleton_schema(self):
         """Test making a new schema skeleton"""
@@ -267,7 +270,7 @@ def test_remove_schema_notfound_configs_childschema(self):
         even when they're in a group
         """
         self.schema_obj.schema = {
-            "definitions": {
+            "$defs": {
                 "subSchemaId": {
                     "properties": {"foo": {"type": "string"}, "bar": {"type": "string"}},
                     "required": ["foo"],
@@ -277,8 +280,8 @@ def test_remove_schema_notfound_configs_childschema(self):
         self.schema_obj.pipeline_params = {"bar": True}
         self.schema_obj.no_prompts = True
         params_removed = self.schema_obj.remove_schema_notfound_configs()
-        assert len(self.schema_obj.schema["definitions"]["subSchemaId"]["properties"]) == 1
-        assert "required" not in self.schema_obj.schema["definitions"]["subSchemaId"]
+        assert len(self.schema_obj.schema["$defs"]["subSchemaId"]["properties"]) == 1
+        assert "required" not in self.schema_obj.schema["$defs"]["subSchemaId"]
         assert len(params_removed) == 1
         assert "foo" in params_removed
 

From 04fabe5d38eb2b948903645137d98a37cd532567 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 27 Aug 2024 10:26:47 +0200
Subject: [PATCH 42/63] ruff

---
 nf_core/pipelines/launch.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/nf_core/pipelines/launch.py b/nf_core/pipelines/launch.py
index a14a8d6d72..a80639ea94 100644
--- a/nf_core/pipelines/launch.py
+++ b/nf_core/pipelines/launch.py
@@ -279,7 +279,6 @@ def merge_nxf_flag_schema(self):
         # Add the new defintion to the allOf key so that it's included in validation
         # Put it at the start of the list so that it comes first
 
-
     def prompt_web_gui(self):
         """Ask whether to use the web-based or cli wizard to collect params"""
         log.info(

From 0649a756bd4727926951be3a17b6bf643ea93dae Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 27 Aug 2024 10:31:07 +0200
Subject: [PATCH 43/63] readd file exists check

---
 tests/pipelines/lint/test_files_exist.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/pipelines/lint/test_files_exist.py b/tests/pipelines/lint/test_files_exist.py
index 85ba817536..65217903f8 100644
--- a/tests/pipelines/lint/test_files_exist.py
+++ b/tests/pipelines/lint/test_files_exist.py
@@ -62,7 +62,7 @@ def test_files_exist_pass_conditional(self):
         lib_dir.mkdir()
         (lib_dir / "nfcore_external_java_deps.jar").touch()
         results = lint_obj.files_exist()
-        assert results["failed"] == []
+        assert results["failed"] == ["File must be removed: `lib/nfcore_external_java_deps.jar`"]
         assert results["ignored"] == []
 
     def test_files_exist_fail_conditional(self):

From 9fd98692e9eb22514f9a107509b12c4cfc2df14e Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 27 Aug 2024 10:41:23 +0200
Subject: [PATCH 44/63] fix lint test

---
 tests/subworkflows/test_lint.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/subworkflows/test_lint.py b/tests/subworkflows/test_lint.py
index c8b97fd0b0..56574b865c 100644
--- a/tests/subworkflows/test_lint.py
+++ b/tests/subworkflows/test_lint.py
@@ -22,7 +22,7 @@ def test_subworkflows_lint_empty(self):
         """Test linting a pipeline with no subworkflows installed"""
         self.subworkflow_remove.remove("utils_nextflow_pipeline", force=True)
         self.subworkflow_remove.remove("utils_nfcore_pipeline", force=True)
-        self.subworkflow_remove.remove("utils_nfvalidation_plugin", force=True)
+        self.subworkflow_remove.remove("utils_nfschema_plugin", force=True)
         nf_core.subworkflows.SubworkflowLint(directory=self.pipeline_dir)
         assert "No subworkflows from https://github.com/nf-core/modules.git installed in pipeline" in self.caplog.text
 

From 6cccc1e8aa650ccc13f4e9159265d42f84f9f9e5 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 27 Aug 2024 11:16:07 +0200
Subject: [PATCH 45/63] update textual snapshots

---
 .../__snapshots__/test_create_app.ambr        | 762 +++++++++---------
 1 file changed, 381 insertions(+), 381 deletions(-)

diff --git a/tests/pipelines/__snapshots__/test_create_app.ambr b/tests/pipelines/__snapshots__/test_create_app.ambr
index 08676899a1..3ed8349ee1 100644
--- a/tests/pipelines/__snapshots__/test_create_app.ambr
+++ b/tests/pipelines/__snapshots__/test_create_app.ambr
@@ -851,257 +851,257 @@
           font-weight: 700;
       }
   
-      .terminal-988282695-matrix {
+      .terminal-2541420365-matrix {
           font-family: Fira Code, monospace;
           font-size: 20px;
           line-height: 24.4px;
           font-variant-east-asian: full-width;
       }
   
-      .terminal-988282695-title {
+      .terminal-2541420365-title {
           font-size: 18px;
           font-weight: bold;
           font-family: arial;
       }
   
-      .terminal-988282695-r1 { fill: #c5c8c6 }
-  .terminal-988282695-r2 { fill: #e3e3e3 }
-  .terminal-988282695-r3 { fill: #989898 }
-  .terminal-988282695-r4 { fill: #e1e1e1 }
-  .terminal-988282695-r5 { fill: #4ebf71;font-weight: bold }
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From 2ccbdd9b64bd9e3cb2792408a3920c6bc314dba4 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 27 Aug 2024 11:37:05 +0200
Subject: [PATCH 46/63] skip linting before and after Text params for custom
 pipelines

---
 nf_core/pipelines/create/templatefeatures.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml
index 7fd7880cba..057b5a6f33 100644
--- a/nf_core/pipelines/create/templatefeatures.yml
+++ b/nf_core/pipelines/create/templatefeatures.yml
@@ -141,6 +141,10 @@ is_nfcore:
     nextflow_config:
       - "manifest.name"
       - "manifest.homePage"
+      - "validation.help.beforeText"
+      - "validation.help.afterText"
+      - "validation.sumary.beforeText"
+      - "validation.sumary.afterText"
     multiqc_config:
       - "report_comment"
   nfcore_pipelines: False

From ed01eba16b92d98db06eaa10bfe6282cd41821df Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 27 Aug 2024 11:42:50 +0200
Subject: [PATCH 47/63] typo

---
 nf_core/pipelines/create/templatefeatures.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml
index 057b5a6f33..940d124085 100644
--- a/nf_core/pipelines/create/templatefeatures.yml
+++ b/nf_core/pipelines/create/templatefeatures.yml
@@ -143,8 +143,8 @@ is_nfcore:
       - "manifest.homePage"
       - "validation.help.beforeText"
       - "validation.help.afterText"
-      - "validation.sumary.beforeText"
-      - "validation.sumary.afterText"
+      - "validation.summary.beforeText"
+      - "validation.summary.afterText"
     multiqc_config:
       - "report_comment"
   nfcore_pipelines: False

From 1b597f17c3ea20e5932f1b92b72887190a5a9a9c Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
Date: Tue, 27 Aug 2024 12:38:04 +0200
Subject: [PATCH 48/63] Update nf_core/pipeline-template/nextflow.config
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
---
 nf_core/pipeline-template/nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index b4c7f41134..c9437d45f2 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -275,7 +275,7 @@ validation {
     help {
         enabled = true
         command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
-        {% if is_nfcore %}
+        {%- if is_nfcore %}
         beforeText = """
 -\033[2m----------------------------------------------------\033[0m-
                                         \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m

From 93cc41be471cd4e50eb83ed5547e4d65496b65fc Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
Date: Tue, 27 Aug 2024 12:40:36 +0200
Subject: [PATCH 49/63] Update
 nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
---
 .../subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
index 4fcda5a7da..92aaa52a11 100644
--- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
@@ -130,7 +130,7 @@ workflow PIPELINE_COMPLETION {
     {% if multiqc %}multiqc_report  //  string: Path to MultiQC report{% endif %}
 
     main:
-    {% if nf_schema %}
+    {%- if nf_schema %}
     summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
     {% else %}
     summary_params = [:]

From 6e358f3fdb2e2a893a87e7a642e61d788d4c8d8c Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
Date: Tue, 27 Aug 2024 12:40:44 +0200
Subject: [PATCH 50/63] Update
 nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
---
 .../subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
index 92aaa52a11..71c96dea1c 100644
--- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
@@ -132,7 +132,7 @@ workflow PIPELINE_COMPLETION {
     main:
     {%- if nf_schema %}
     summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
-    {% else %}
+    {%- else %}
     summary_params = [:]
     {% endif %}
 

From dbe9318ac9eb698f6c4d53c2768217289574ba47 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
Date: Tue, 27 Aug 2024 12:40:53 +0200
Subject: [PATCH 51/63] Update
 nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
---
 .../subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
index 71c96dea1c..ae66f3674c 100644
--- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
@@ -134,7 +134,7 @@ workflow PIPELINE_COMPLETION {
     summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
     {%- else %}
     summary_params = [:]
-    {% endif %}
+    {%- endif %}
 
     //
     // Completion email and summary

From 4025b546d6a9090099636fe821e489d1fd07ba45 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
Date: Tue, 27 Aug 2024 12:41:26 +0200
Subject: [PATCH 52/63] Update nf_core/pipelines/create/templatefeatures.yml
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
---
 nf_core/pipelines/create/templatefeatures.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml
index 940d124085..8d31852ab9 100644
--- a/nf_core/pipelines/create/templatefeatures.yml
+++ b/nf_core/pipelines/create/templatefeatures.yml
@@ -260,7 +260,7 @@ nf_schema:
   skippable_paths:
     - "subworkflows/nf-core/utils_nfschema_plugin"
   short_description: "Use nf-schema"
-  description: "Use nf-schema for this pipeline."
+  description: "Use the nf-schema Nextflow plugin for this pipeline."
   help_text: |
     nf-schema is used to validate input parameters based on a JSON schema.
     It also provides helper functionality to create help messages, get a summary

From 679de826cfd3e6526d718e2d95a8ba2da057d512 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
Date: Tue, 27 Aug 2024 12:42:58 +0200
Subject: [PATCH 53/63] Update tests/pipelines/lint/test_plugin_includes.py
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
---
 tests/pipelines/lint/test_plugin_includes.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/pipelines/lint/test_plugin_includes.py b/tests/pipelines/lint/test_plugin_includes.py
index ca14d5456d..8eb31e2671 100644
--- a/tests/pipelines/lint/test_plugin_includes.py
+++ b/tests/pipelines/lint/test_plugin_includes.py
@@ -3,7 +3,7 @@
 from ..test_lint import TestLint
 
 
-class TestLintNextflowConfig(TestLint):
+class TestLintPluginIncludes(TestLint):
     def setUp(self) -> None:
         super().setUp()
         self.new_pipeline = self._make_pipeline_copy()

From 3ac1bd8e42a986381c12941b94ce786f8fb393f4 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 27 Aug 2024 12:46:56 +0200
Subject: [PATCH 54/63] review suggestions

---
 nf_core/pipeline-template/modules.json        |  2 +-
 .../nf-core/utils_nextflow_pipeline/main.nf   |  2 +-
 nf_core/pipelines/lint/files_exist.py         | 22 ++-----------------
 tests/pipelines/lint/test_files_exist.py      | 21 ------------------
 4 files changed, 4 insertions(+), 43 deletions(-)

diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json
index ec1cf1d963..9f44a4a672 100644
--- a/nf_core/pipeline-template/modules.json
+++ b/nf_core/pipeline-template/modules.json
@@ -23,7 +23,7 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "2aacc9ef22bfc627b18eca17e9a3bb13c58aab64",
+                        "git_sha": "0710581f16d6f4e6b27ab6f410757c8259fdd6f4",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
index b54fc16c71..28e32b200e 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
@@ -98,7 +98,7 @@ def checkCondaChannels() {
 
     // Check that all channels are present
     // This channel list is ordered by required channel priority.
-    def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults']
+    def required_channels_in_order = ['conda-forge', 'bioconda']
     def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean
 
     // Check that they are in the right order
diff --git a/nf_core/pipelines/lint/files_exist.py b/nf_core/pipelines/lint/files_exist.py
index 7bfbae8ec9..99f2d1b937 100644
--- a/nf_core/pipelines/lint/files_exist.py
+++ b/nf_core/pipelines/lint/files_exist.py
@@ -1,6 +1,6 @@
 import logging
 from pathlib import Path
-from typing import Dict, List, Tuple, Union
+from typing import Dict, List, Union
 
 log = logging.getLogger(__name__)
 
@@ -201,7 +201,6 @@ def files_exist(self) -> Dict[str, List[str]]:
         Path("lib", "nfcore_external_java_deps.jar"),
     ]
     files_warn_ifexists = [Path(".travis.yml")]
-    files_fail_ifinconfig: List[Tuple[Path, List[Dict[str, str]]]] = []
 
     # Remove files that should be ignored according to the linting config
     ignore_files = self.lint_config.get("files_exist", []) if self.lint_config is not None else []
@@ -240,24 +239,7 @@ def pf(file_path: Union[str, Path]) -> Path:
             failed.append(f"File must be removed: {self._wrap_quotes(file)}")
         else:
             passed.append(f"File not found check: {self._wrap_quotes(file)}")
-    # Files that cause an error if they exists together with a certain entry in nextflow.config
-    for file_cond in files_fail_ifinconfig:
-        if str(file_cond[0]) in ignore_files:
-            continue
-        in_config = False
-        for condition in file_cond[1]:
-            config_key, config_value = list(condition.items())[0]
-            if config_key in self.nf_config and config_value in self.nf_config[config_key]:
-                log.debug(f"Found {config_key} in nextflow.config with value {config_value}")
-                in_config = True
-        if pf(file_cond[0]).is_file() and in_config:
-            failed.append(f"File must be removed: {self._wrap_quotes(file_cond[0])}")
-        elif pf(file_cond[0]).is_file() and not in_config:
-            passed.append(f"File found check: {self._wrap_quotes(file_cond[0])}")
-        elif not pf(file_cond[0]).is_file() and not in_config:
-            failed.append(f"File not found check: {self._wrap_quotes(file_cond[0])}")
-        elif not pf(file_cond[0]).is_file() and in_config:
-            passed.append(f"File not found check: {self._wrap_quotes(file_cond[0])}")
+
     # Files that cause a warning if they exist
     for file in files_warn_ifexists:
         if str(file) in ignore_files:
diff --git a/tests/pipelines/lint/test_files_exist.py b/tests/pipelines/lint/test_files_exist.py
index 65217903f8..97dd346cdf 100644
--- a/tests/pipelines/lint/test_files_exist.py
+++ b/tests/pipelines/lint/test_files_exist.py
@@ -54,27 +54,6 @@ def test_files_exist_pass(self):
         results = lint_obj.files_exist()
         assert results["failed"] == []
 
-    def test_files_exist_pass_conditional(self):
-        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
-        lint_obj._load()
-        lint_obj.nf_config["plugins"] = []
-        lib_dir = Path(self.new_pipeline, "lib")
-        lib_dir.mkdir()
-        (lib_dir / "nfcore_external_java_deps.jar").touch()
-        results = lint_obj.files_exist()
-        assert results["failed"] == ["File must be removed: `lib/nfcore_external_java_deps.jar`"]
-        assert results["ignored"] == []
-
-    def test_files_exist_fail_conditional(self):
-        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
-        lint_obj._load()
-        lib_dir = Path(self.new_pipeline, "lib")
-        lib_dir.mkdir()
-        (lib_dir / "nfcore_external_java_deps.jar").touch()
-        results = lint_obj.files_exist()
-        assert results["failed"] == ["File must be removed: `lib/nfcore_external_java_deps.jar`"]
-        assert results["ignored"] == []
-
     def test_files_exist_pass_conditional_nfschema(self):
         # replace nf-validation with nf-schema in nextflow.config
         with open(Path(self.new_pipeline, "nextflow.config")) as f:

From d4266c0bb19027db883107d47a50ace106affff7 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 27 Aug 2024 13:32:53 +0200
Subject: [PATCH 55/63] use latest version of utils_nextflow_pipeline

---
 nf_core/pipeline-template/modules.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json
index 9f44a4a672..caeaac2fdf 100644
--- a/nf_core/pipeline-template/modules.json
+++ b/nf_core/pipeline-template/modules.json
@@ -23,7 +23,7 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "0710581f16d6f4e6b27ab6f410757c8259fdd6f4",
+                        "git_sha": "16f913a1ea8bb2cc48ccfc0b3b9406c5b3333799",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {

From bc20099658a5a66e2ca3cc982b2e7cc4735bbab8 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 27 Aug 2024 13:52:18 +0200
Subject: [PATCH 56/63] make help params snake_case

---
 nf_core/pipeline-template/nextflow.config | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index c9437d45f2..8818ec54db 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -40,8 +40,8 @@ params {
     monochrome_logs              = false
     hook_url                     = null
     {% if nf_schema %}help                         = false
-    helpFull                     = false
-    showHidden                   = false{% endif %}
+    help_full                    = false
+    show_hidden                  = false{% endif %}
     version                      = false
     {% if test_config %}pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'{% endif %}
 
@@ -275,6 +275,8 @@ validation {
     help {
         enabled = true
         command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
+        fullParameter = "help_full"
+        showHiddenParameter = "show_hidden"
         {%- if is_nfcore %}
         beforeText = """
 -\033[2m----------------------------------------------------\033[0m-

From 829d594be396edd5a2d54d8536972689b64b5fe6 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
Date: Tue, 27 Aug 2024 14:33:58 +0200
Subject: [PATCH 57/63] Update nf_core/pipelines/create/templatefeatures.yml
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
---
 nf_core/pipelines/create/templatefeatures.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml
index 8d31852ab9..7388ecc7ba 100644
--- a/nf_core/pipelines/create/templatefeatures.yml
+++ b/nf_core/pipelines/create/templatefeatures.yml
@@ -262,7 +262,7 @@ nf_schema:
   short_description: "Use nf-schema"
   description: "Use the nf-schema Nextflow plugin for this pipeline."
   help_text: |
-    nf-schema is used to validate input parameters based on a JSON schema.
+    [nf-schema](https://nextflow-io.github.io/nf-schema/latest/) is used to validate input parameters based on a JSON schema.
     It also provides helper functionality to create help messages, get a summary
     of changed parameters and validate and convert a samplesheet to a channel.
   nfcore_pipelines: True

From 1ff7cbcfe58015b636c8edd852ac422e74598770 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
Date: Tue, 27 Aug 2024 14:34:25 +0200
Subject: [PATCH 58/63] Update nf_core/pipelines/lint/plugin_includes.py
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
---
 nf_core/pipelines/lint/plugin_includes.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/nf_core/pipelines/lint/plugin_includes.py b/nf_core/pipelines/lint/plugin_includes.py
index 6a57b1d280..4fc40ae26c 100644
--- a/nf_core/pipelines/lint/plugin_includes.py
+++ b/nf_core/pipelines/lint/plugin_includes.py
@@ -16,10 +16,10 @@ def plugin_includes(self) -> Dict[str, List[str]]:
     config_plugins = [plugin.split("@")[0] for plugin in ast.literal_eval(self.nf_config.get("plugins", "[]"))]
     validation_plugin = "nf-validation" if "nf-validation" in config_plugins else "nf-schema"
 
-    passed: list[str] = []
-    warned: list[str] = []
-    failed: list[str] = []
-    ignored: list[str] = []
+    passed: List[str] = []
+    warned: List[str] = []
+    failed: List[str] = []
+    ignored: List[str] = []
 
     plugin_include_pattern = re.compile(r"^include\s*{[^}]+}\s*from\s*[\"']plugin/([^\"']+)[\"']\s*$", re.MULTILINE)
     workflow_files = [

From aed94601c7241546def06c226758c96688587cb2 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 27 Aug 2024 14:37:03 +0200
Subject: [PATCH 59/63] apply review suggestions

---
 nf_core/pipelines/lint/nextflow_config.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py
index 2159d7939a..790fc21797 100644
--- a/nf_core/pipelines/lint/nextflow_config.py
+++ b/nf_core/pipelines/lint/nextflow_config.py
@@ -168,8 +168,6 @@ def nextflow_config(self) -> Dict[str, List[str]]:
     if "nf-validation" in found_plugins or "nf-schema" in found_plugins:
         if "nf-validation" in found_plugins and "nf-schema" in found_plugins:
             failed.append("nextflow.config contains both nf-validation and nf-schema")
-        if "nf-validation" not in found_plugins and "nf-schema" not in found_plugins:
-            warned.append("nextflow.config does not contain `nf-validation` or `nf-schema` in the plugins scope")
 
         if "nf-schema" in found_plugins:
             passed.append("Found nf-schema plugin")

From 4407901d8c7a039d97ee45390ead386611de42e2 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 27 Aug 2024 14:41:53 +0200
Subject: [PATCH 60/63] update utils_nextflow_pipeline commit messages

---
 nf_core/pipeline-template/modules.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json
index caeaac2fdf..367202155a 100644
--- a/nf_core/pipeline-template/modules.json
+++ b/nf_core/pipeline-template/modules.json
@@ -23,7 +23,7 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "16f913a1ea8bb2cc48ccfc0b3b9406c5b3333799",
+                        "git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {

From 330e43c76109f500ee88bdeddd0ef578751d8376 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 27 Aug 2024 14:48:37 +0200
Subject: [PATCH 61/63] update ignoring of help params

---
 nf_core/pipelines/schema.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index 6c1c198bb8..95ed5e5b6e 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -92,7 +92,11 @@ def _update_validation_plugin_from_config(self) -> None:
         # Previous versions of nf-schema used "defs", but it's advised to use "$defs"
         if plugin == "nf-schema":
             self.defs_notation = "$defs"
-            ignored_params = ["help", "helpFull", "showHidden"]  # Help parameter should be ignored by default
+            ignored_params = [
+                conf.get("validation.help.shortParameter", "help"),
+                conf.get("validation.help.fullParameter", "helpFull"),
+                conf.get("validation.help.showHiddenParameter", "showHidden"),
+            ]  # Help parameter should be ignored by default
             ignored_params_config = conf.get("validation", {}).get("defaultIgnoreParams", [])
             if len(ignored_params_config) > 0:
                 ignored_params.extend(ignored_params_config)

From 3600db75edf62709fcd48c6174c6b698c95c93f3 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 27 Aug 2024 14:57:12 +0200
Subject: [PATCH 62/63] update file exists docstring

---
 nf_core/pipelines/lint/files_exist.py | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/nf_core/pipelines/lint/files_exist.py b/nf_core/pipelines/lint/files_exist.py
index 99f2d1b937..bd25ff33d0 100644
--- a/nf_core/pipelines/lint/files_exist.py
+++ b/nf_core/pipelines/lint/files_exist.py
@@ -87,6 +87,7 @@ def files_exist(self) -> Dict[str, List[str]]:
         lib/Workflow.groovy
         lib/WorkflowMain.groovy
         lib/WorkflowPIPELINE.groovy
+        lib/nfcore_external_java_deps.jar
         parameters.settings.json
         pipeline_template.yml # saving information in .nf-core.yml
         Singularity
@@ -98,12 +99,6 @@ def files_exist(self) -> Dict[str, List[str]]:
 
         .travis.yml
 
-    Files that *must not* be present if a certain entry is present in ``nextflow.config``:
-
-    .. code-block:: bash
-
-        lib/nfcore_external_java_deps.jar # if "nf-validation" is in nextflow.config
-
     .. tip:: You can configure the ``nf-core pipelines lint`` tests to ignore any of these checks by setting
             the ``files_exist`` key as follows in your ``.nf-core.yml`` config file. For example:
 

From e816fafe8a1c984bf54b7f78979c35f494b1a2d9 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 27 Aug 2024 15:32:20 +0200
Subject: [PATCH 63/63] update snapshot

---
 .../__snapshots__/test_create_app.ambr        | 504 +++++++++---------
 1 file changed, 252 insertions(+), 252 deletions(-)

diff --git a/tests/pipelines/__snapshots__/test_create_app.ambr b/tests/pipelines/__snapshots__/test_create_app.ambr
index 3ed8349ee1..af88080668 100644
--- a/tests/pipelines/__snapshots__/test_create_app.ambr
+++ b/tests/pipelines/__snapshots__/test_create_app.ambr
@@ -2233,255 +2233,255 @@
           font-weight: 700;
       }
   
-      .terminal-3458551717-matrix {
+      .terminal-1373392807-matrix {
           font-family: Fira Code, monospace;
           font-size: 20px;
           line-height: 24.4px;
           font-variant-east-asian: full-width;
       }
   
-      .terminal-3458551717-title {
+      .terminal-1373392807-title {
           font-size: 18px;
           font-weight: bold;
           font-family: arial;
       }
   
-      .terminal-3458551717-r1 { fill: #c5c8c6 }
-  .terminal-3458551717-r2 { fill: #e3e3e3 }
-  .terminal-3458551717-r3 { fill: #989898 }
-  .terminal-3458551717-r4 { fill: #e1e1e1 }
-  .terminal-3458551717-r5 { fill: #4ebf71;font-weight: bold }
-  .terminal-3458551717-r6 { fill: #1e1e1e }
-  .terminal-3458551717-r7 { fill: #507bb3 }
-  .terminal-3458551717-r8 { fill: #e2e2e2 }
-  .terminal-3458551717-r9 { fill: #808080 }
-  .terminal-3458551717-r10 { fill: #dde6ed;font-weight: bold }
-  .terminal-3458551717-r11 { fill: #001541 }
-  .terminal-3458551717-r12 { fill: #14191f }
-  .terminal-3458551717-r13 { fill: #454a50 }
-  .terminal-3458551717-r14 { fill: #7ae998 }
-  .terminal-3458551717-r15 { fill: #e2e3e3;font-weight: bold }
-  .terminal-3458551717-r16 { fill: #0a180e;font-weight: bold }
-  .terminal-3458551717-r17 { fill: #000000 }
-  .terminal-3458551717-r18 { fill: #008139 }
-  .terminal-3458551717-r19 { fill: #fea62b;font-weight: bold }
-  .terminal-3458551717-r20 { fill: #a7a9ab }
-  .terminal-3458551717-r21 { fill: #e2e3e3 }
+      .terminal-1373392807-r1 { fill: #c5c8c6 }
+  .terminal-1373392807-r2 { fill: #e3e3e3 }
+  .terminal-1373392807-r3 { fill: #989898 }
+  .terminal-1373392807-r4 { fill: #e1e1e1 }
+  .terminal-1373392807-r5 { fill: #4ebf71;font-weight: bold }
+  .terminal-1373392807-r6 { fill: #1e1e1e }
+  .terminal-1373392807-r7 { fill: #507bb3 }
+  .terminal-1373392807-r8 { fill: #e2e2e2 }
+  .terminal-1373392807-r9 { fill: #808080 }
+  .terminal-1373392807-r10 { fill: #dde6ed;font-weight: bold }
+  .terminal-1373392807-r11 { fill: #001541 }
+  .terminal-1373392807-r12 { fill: #14191f }
+  .terminal-1373392807-r13 { fill: #454a50 }
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