Merge branch 'dev' into LouisLeNezet-config

Author: LouisLeNezet

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.4
+    rev: v0.8.0
     hooks:
       - id: ruff # linter
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix

CHANGELOG.md

@@ -10,6 +10,7 @@
 - fix workflow_dispatch trigger and parse more review comments in awsfulltest ([#3235](https://github.com/nf-core/tools/pull/3235))
 - Add resource limits to Gitpod profile([#3255](https://github.com/nf-core/tools/pull/3255))
 - Fix a typo ([#3268](https://github.com/nf-core/tools/pull/3268))
+- Remove `def` from `nextflow.config` and add `trace_report_suffix` param ([#3296](https://github.com/nf-core/tools/pull/3296))
 
 ### Download
 
@@ -25,6 +26,8 @@
 
 ### Subworkflows
 
+- Add `nf-core subworkflows patch` command ([#2861](https://github.com/nf-core/tools/pull/2861))
+
 ### General
 
 - Include .nf-core.yml in `nf-core pipelines bump-version` ([#3220](https://github.com/nf-core/tools/pull/3220))
@@ -44,6 +47,7 @@
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.7.4 ([#3282](https://github.com/nf-core/tools/pull/3282))
 - Update codecov/codecov-action action to v5 ([#3283](https://github.com/nf-core/tools/pull/3283))
 - Update python:3.12-slim Docker digest to 2a6386a ([#3284](https://github.com/nf-core/tools/pull/3284))
+- Update pre-commit hook astral-sh/ruff-pre-commit to v0.8.0 ([#3299](https://github.com/nf-core/tools/pull/3299))
 
 ## [v3.0.2 - Titanium Tapir Patch](https://github.com/nf-core/tools/releases/tag/3.0.2) - [2024-10-11]
 

nf_core/__main__.py

@@ -1024,7 +1024,7 @@ def command_modules_update(
     default=".",
     help=r"Pipeline directory. [dim]\[default: current working directory][/]",
 )
-@click.option("-r", "--remove", is_flag=True, default=False)
+@click.option("-r", "--remove", is_flag=True, default=False, help="Remove an existent patch file and regenerate it.")
 def command_modules_patch(ctx, tool, directory, remove):
     """
     Create a patch file for minor changes in a module
@@ -1567,6 +1567,43 @@ def command_subworkflows_install(ctx, subworkflow, directory, prompt, force, sha
     subworkflows_install(ctx, subworkflow, directory, prompt, force, sha)
 
 
+# nf-core subworkflows patch
+@subworkflows.command("patch")
+@click.pass_context
+@click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
+@click.option(
+    "-d",
+    "--dir",
+    type=click.Path(exists=True),
+    default=".",
+    help=r"Pipeline directory. [dim]\[default: current working directory][/]",
+)
+@click.option("-r", "--remove", is_flag=True, default=False, help="Remove an existent patch file and regenerate it.")
+def subworkflows_patch(ctx, tool, dir, remove):
+    """
+    Create a patch file for minor changes in a subworkflow
+
+    Checks if a subworkflow has been modified locally and creates a patch file
+    describing how the module has changed from the remote version
+    """
+    from nf_core.subworkflows import SubworkflowPatch
+
+    try:
+        subworkflow_patch = SubworkflowPatch(
+            dir,
+            ctx.obj["modules_repo_url"],
+            ctx.obj["modules_repo_branch"],
+            ctx.obj["modules_repo_no_pull"],
+        )
+        if remove:
+            subworkflow_patch.remove(tool)
+        else:
+            subworkflow_patch.patch(tool)
+    except (UserWarning, LookupError) as e:
+        log.error(e)
+        sys.exit(1)
+
+
 # nf-core subworkflows remove
 @subworkflows.command("remove")
 @click.pass_context

nf_core/modules/modules_differ.py renamed to nf_core/components/components_differ.py

@@ -8,7 +8,7 @@
 
 import nf_core.utils
 from nf_core.components.components_command import ComponentCommand
-from nf_core.modules.modules_differ import ModulesDiffer
+from nf_core.components.components_differ import ComponentsDiffer
 from nf_core.modules.modules_json import ModulesJson
 
 log = logging.getLogger(__name__)
@@ -65,7 +65,9 @@ def patch(self, component=None):
         component_fullname = str(Path(self.component_type, self.modules_repo.repo_path, component))
 
         # Verify that the component has an entry in the modules.json file
-        if not self.modules_json.module_present(component, self.modules_repo.remote_url, component_dir):
+        if not self.modules_json.component_present(
+            component, self.modules_repo.remote_url, component_dir, self.component_type
+        ):
             raise UserWarning(
                 f"The '{component_fullname}' {self.component_type[:-1]} does not have an entry in the 'modules.json' file. Cannot compute patch"
             )
@@ -112,7 +114,7 @@ def patch(self, component=None):
         # Write the patch to a temporary location (otherwise it is printed to the screen later)
         patch_temp_path = tempfile.mktemp()
         try:
-            ModulesDiffer.write_diff_file(
+            ComponentsDiffer.write_diff_file(
                 patch_temp_path,
                 component,
                 self.modules_repo.repo_path,
@@ -127,11 +129,13 @@ def patch(self, component=None):
             raise UserWarning(f"{self.component_type[:-1]} '{component_fullname}' is unchanged. No patch to compute")
 
         # Write changes to modules.json
-        self.modules_json.add_patch_entry(component, self.modules_repo.remote_url, component_dir, patch_relpath)
+        self.modules_json.add_patch_entry(
+            self.component_type, component, self.modules_repo.remote_url, component_dir, patch_relpath
+        )
         log.debug(f"Wrote patch path for {self.component_type[:-1]} {component} to modules.json")
 
         # Show the changes made to the module
-        ModulesDiffer.print_diff(
+        ComponentsDiffer.print_diff(
             component,
             self.modules_repo.repo_path,
             component_install_dir,
@@ -166,7 +170,9 @@ def remove(self, component):
         component_fullname = str(Path(self.component_type, component_dir, component))
 
         # Verify that the component has an entry in the modules.json file
-        if not self.modules_json.module_present(component, self.modules_repo.remote_url, component_dir):
+        if not self.modules_json.component_present(
+            component, self.modules_repo.remote_url, component_dir, self.component_type
+        ):
             raise UserWarning(
                 f"The '{component_fullname}' {self.component_type[:-1]} does not have an entry in the 'modules.json' file. Cannot compute patch"
             )
@@ -202,7 +208,7 @@ def remove(self, component):
 
         # Try to apply the patch in reverse and move resulting files to module dir
         temp_component_dir = self.modules_json.try_apply_patch_reverse(
-            component, self.modules_repo.repo_path, patch_relpath, component_path
+            self.component_type, component, self.modules_repo.repo_path, patch_relpath, component_path
         )
         try:
             for file in Path(temp_component_dir).glob("*"):

nf_core/components/patch.py

@@ -68,7 +68,7 @@ def remove(self, component, removed_by=None, removed_components=None, force=Fals
         if not component_dir.exists():
             log.error(f"Installation directory '{component_dir}' does not exist.")
 
-            if modules_json.module_present(component, self.modules_repo.remote_url, repo_path):
+            if modules_json.component_present(component, self.modules_repo.remote_url, repo_path, self.component_type):
                 log.error(f"Found entry for '{component}' in 'modules.json'. Removing...")
                 modules_json.remove_entry(self.component_type, component, self.modules_repo.remote_url, repo_path)
             return False

nf_core/components/remove.py

@@ -9,13 +9,13 @@
 import nf_core.modules.modules_utils
 import nf_core.utils
 from nf_core.components.components_command import ComponentCommand
+from nf_core.components.components_differ import ComponentsDiffer
 from nf_core.components.components_utils import (
     get_components_to_install,
     prompt_component_version_sha,
 )
 from nf_core.components.install import ComponentInstall
 from nf_core.components.remove import ComponentRemove
-from nf_core.modules.modules_differ import ModulesDiffer
 from nf_core.modules.modules_json import ModulesJson
 from nf_core.modules.modules_repo import ModulesRepo
 from nf_core.utils import plural_es, plural_s, plural_y
@@ -223,7 +223,7 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr
                         f"Writing diff file for {self.component_type[:-1]} '{component_fullname}' to '{self.save_diff_fn}'"
                     )
                     try:
-                        ModulesDiffer.write_diff_file(
+                        ComponentsDiffer.write_diff_file(
                             self.save_diff_fn,
                             component,
                             modules_repo.repo_path,
@@ -265,7 +265,7 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr
                         self.manage_changes_in_linked_components(component, modules_to_update, subworkflows_to_update)
 
                 elif self.show_diff:
-                    ModulesDiffer.print_diff(
+                    ComponentsDiffer.print_diff(
                         component,
                         modules_repo.repo_path,
                         component_dir,
@@ -313,7 +313,7 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr
 
         if self.save_diff_fn:
             # Write the modules.json diff to the file
-            ModulesDiffer.append_modules_json_diff(
+            ComponentsDiffer.append_modules_json_diff(
                 self.save_diff_fn,
                 old_modules_json,
                 self.modules_json.get_modules_json(),
@@ -449,7 +449,9 @@ def get_single_component_info(self, component):
                 self.modules_repo.setup_branch(current_branch)
 
         # If there is a patch file, get its filename
-        patch_fn = self.modules_json.get_patch_fn(component, self.modules_repo.remote_url, install_dir)
+        patch_fn = self.modules_json.get_patch_fn(
+            self.component_type, component, self.modules_repo.remote_url, install_dir
+        )
 
         return (self.modules_repo, component, sha, patch_fn)
 
@@ -695,7 +697,12 @@ def get_all_components_info(self, branch=None):
 
         # Add patch filenames to the components that have them
         components_info = [
-            (repo, comp, sha, self.modules_json.get_patch_fn(comp, repo.remote_url, repo.repo_path))
+            (
+                repo,
+                comp,
+                sha,
+                self.modules_json.get_patch_fn(self.component_type, comp, repo.remote_url, repo.repo_path),
+            )
             for repo, comp, sha in components_info
         ]
 
@@ -810,7 +817,9 @@ def try_apply_patch(
         shutil.copytree(component_install_dir, temp_component_dir)
 
         try:
-            new_files = ModulesDiffer.try_apply_patch(component, repo_path, patch_path, temp_component_dir)
+            new_files = ComponentsDiffer.try_apply_patch(
+                self.component_type, component, repo_path, patch_path, temp_component_dir
+            )
         except LookupError:
             # Patch failed. Save the patch file by moving to the install dir
             shutil.move(patch_path, Path(component_install_dir, patch_path.relative_to(component_dir)))
@@ -828,7 +837,7 @@ def try_apply_patch(
 
         # Create the new patch file
         log.debug("Regenerating patch file")
-        ModulesDiffer.write_diff_file(
+        ComponentsDiffer.write_diff_file(
             Path(temp_component_dir, patch_path.relative_to(component_dir)),
             component,
             repo_path,
@@ -848,7 +857,12 @@ def try_apply_patch(
 
         # Add the patch file to the modules.json file
         self.modules_json.add_patch_entry(
-            component, self.modules_repo.remote_url, repo_path, patch_relpath, write_file=write_file
+            self.component_type,
+            component,
+            self.modules_repo.remote_url,
+            repo_path,
+            patch_relpath,
+            write_file=write_file,
         )
 
         return True

nf_core/components/update.py

@@ -15,8 +15,8 @@
 
 import nf_core
 import nf_core.modules.modules_utils
+from nf_core.components.components_differ import ComponentsDiffer
 from nf_core.components.nfcore_component import NFCoreComponent
-from nf_core.modules.modules_differ import ModulesDiffer
 
 log = logging.getLogger(__name__)
 
@@ -50,7 +50,8 @@ def main_nf(
     # otherwise read the lines directly from the module
     lines: List[str] = []
     if module.is_patched:
-        lines = ModulesDiffer.try_apply_patch(
+        lines = ComponentsDiffer.try_apply_patch(
+            module.component_type,
             module.component_name,
             module_lint_object.modules_repo.repo_path,
             module.patch_path,

nf_core/modules/lint/main_nf.py

@@ -6,9 +6,9 @@
 import ruamel.yaml
 from jsonschema import exceptions, validators
 
+from nf_core.components.components_differ import ComponentsDiffer
 from nf_core.components.lint import ComponentLint, LintExceptionError
 from nf_core.components.nfcore_component import NFCoreComponent
-from nf_core.modules.modules_differ import ModulesDiffer
 
 log = logging.getLogger(__name__)
 
@@ -46,7 +46,8 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> None
     # Check if we have a patch file, get original file in that case
     meta_yaml = read_meta_yml(module_lint_object, module)
     if module.is_patched and module_lint_object.modules_repo.repo_path is not None:
-        lines = ModulesDiffer.try_apply_patch(
+        lines = ComponentsDiffer.try_apply_patch(
+            module.component_type,
             module.component_name,
             module_lint_object.modules_repo.repo_path,
             module.patch_path,
@@ -207,7 +208,8 @@ def read_meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) ->
     yaml.preserve_quotes = True
     # Check if we have a patch file, get original file in that case
     if module.is_patched:
-        lines = ModulesDiffer.try_apply_patch(
+        lines = ComponentsDiffer.try_apply_patch(
+            module.component_type,
             module.component_name,
             module_lint_object.modules_repo.repo_path,
             module.patch_path,

nf_core/modules/lint/meta_yml.py

@@ -7,7 +7,7 @@
 from pathlib import Path
 
 import nf_core.modules.modules_repo
-from nf_core.modules.modules_differ import ModulesDiffer
+from nf_core.components.components_differ import ComponentsDiffer
 
 
 def module_changes(module_lint_object, module):
@@ -30,7 +30,8 @@ def module_changes(module_lint_object, module):
         tempdir = tempdir_parent / "tmp_module_dir"
         shutil.copytree(module.component_dir, tempdir)
         try:
-            new_lines = ModulesDiffer.try_apply_patch(
+            new_lines = ComponentsDiffer.try_apply_patch(
+                module.component_type,
                 module.component_name,
                 module.org,
                 module.patch_path,