From 611f8f4fc104e876bcc549e0b868222367a96223 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Thu, 4 Jul 2024 12:18:12 +0200
Subject: [PATCH] use param --fix to update the meta.yml

---
 nf_core/__main__.py                 | 8 +++-----
 nf_core/components/lint/__init__.py | 4 ++--
 nf_core/modules/lint/__init__.py    | 6 +++---
 nf_core/modules/lint/meta_yml.py    | 4 ++--
 tests/modules/lint.py               | 2 +-
 5 files changed, 11 insertions(+), 13 deletions(-)

diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index 5d34163cb5..d258d73c39 100644
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -1579,10 +1579,8 @@ def test_module(ctx, tool, dir, no_prompts, update, once, profile):
     is_flag=True,
     help="Fix the module version if a newer version is available",
 )
-@click.option(
-    "--update-meta-yml", is_flag=True, help="Update the meta.yml file with the correct format of input and outputs"
-)
-def modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed, sort_by, fix_version, update_meta_yml):
+@click.option("--fix", is_flag=True, help="Fix all linting tests if possible.")
+def modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed, sort_by, fix_version, fix):
     """
     Lint one or more modules in a directory.
 
@@ -1599,7 +1597,7 @@ def modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed,
         module_lint = ModuleLint(
             dir,
             fail_warned=fail_warned,
-            update_meta_yml=update_meta_yml,
+            fix=fix,
             registry=ctx.params["registry"],
             remote_url=ctx.obj["modules_repo_url"],
             branch=ctx.obj["modules_repo_branch"],
diff --git a/nf_core/components/lint/__init__.py b/nf_core/components/lint/__init__.py
index b4194e768e..0e3aba23f7 100644
--- a/nf_core/components/lint/__init__.py
+++ b/nf_core/components/lint/__init__.py
@@ -56,7 +56,7 @@ def __init__(
         component_type,
         dir,
         fail_warned=False,
-        update_meta_yml=False,
+        fix=False,
         remote_url=None,
         branch=None,
         no_pull=False,
@@ -73,7 +73,7 @@ def __init__(
         )
 
         self.fail_warned = fail_warned
-        self.update_meta_yml = update_meta_yml
+        self.fix = fix
         self.passed = []
         self.warned = []
         self.failed = []
diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py
index f6c2069bda..58a4c47159 100644
--- a/nf_core/modules/lint/__init__.py
+++ b/nf_core/modules/lint/__init__.py
@@ -47,7 +47,7 @@ def __init__(
         self,
         dir,
         fail_warned=False,
-        update_meta_yml=False,
+        fix=False,
         remote_url=None,
         branch=None,
         no_pull=False,
@@ -58,7 +58,7 @@ def __init__(
             component_type="modules",
             dir=dir,
             fail_warned=fail_warned,
-            update_meta_yml=update_meta_yml,
+            fix=fix,
             remote_url=remote_url,
             branch=branch,
             no_pull=no_pull,
@@ -224,7 +224,7 @@ def lint_module(self, mod, progress_bar, registry, local=False, fix_version=Fals
             mod.get_inputs_from_main_nf()
             mod.get_outputs_from_main_nf()
             # Update meta.yml file if requested
-            if self.update_meta_yml:
+            if self.fix:
                 self.update_meta_yml_file(mod)
 
             if self.repo_type == "pipeline" and self.modules_json:
diff --git a/nf_core/modules/lint/meta_yml.py b/nf_core/modules/lint/meta_yml.py
index 9c074ba731..c3b5f3f283 100644
--- a/nf_core/modules/lint/meta_yml.py
+++ b/nf_core/modules/lint/meta_yml.py
@@ -117,7 +117,7 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> None
                 module.failed.append(
                     (
                         "correct_meta_inputs",
-                        f"Incorrect inputs specified in module `meta.yml`. Inputs should contain: {correct_inputs}\nRun `nf-core modules lint --update-meta-yml` to update the `meta.yml` file.",
+                        f"Incorrect inputs specified in module `meta.yml`. Inputs should contain: {correct_inputs}\nRun `nf-core modules lint --fix` to update the `meta.yml` file.",
                         module.meta_yml,
                     )
                 )
@@ -155,7 +155,7 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> None
                 module.failed.append(
                     (
                         "correct_meta_outputs",
-                        f"Incorrect outputs specified in module `meta.yml`. Outputs should contain: {correct_outputs}\nRun `nf-core modules lint --update-meta-yml` to update the `meta.yml` file.",
+                        f"Incorrect outputs specified in module `meta.yml`. Outputs should contain: {correct_outputs}\nRun `nf-core modules lint --fix` to update the `meta.yml` file.",
                         module.meta_yml,
                     )
                 )
diff --git a/tests/modules/lint.py b/tests/modules/lint.py
index 7798c0a948..9b6c6a78c3 100644
--- a/tests/modules/lint.py
+++ b/tests/modules/lint.py
@@ -61,7 +61,7 @@ def test_modules_lint_new_modules(self):
 
 def test_modules_lint_update_meta_yml(self):
     """update the meta.yml of a module"""
-    module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules, update_meta_yml=True)
+    module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules, fix=True)
     module_lint.lint(print_results=False, all_modules="fastqc")
     assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
     assert len(module_lint.passed) > 0