Merge branch 'dev' into update-dependencies

CHANGELOG.md

@@ -13,6 +13,7 @@
 
 ### Linting
 
+- Update modules lint test to fail if enable_conda is found ([#2213](https://github.com/nf-core/tools/pull/2213))
 - Read module lint configuration from `.nf-core.yml`, not `.nf-core-lint.yml` ([#2221](https://github.com/nf-core/tools/pull/2221))
 - `nf-core schema lint` now defaults to linting `nextflow_schema.json` if no filename is provided ([#2225](https://github.com/nf-core/tools/pull/2225))
 

nf_core/__main__.py

@@ -1398,7 +1398,9 @@ def build(dir, no_prompts, web_only, url):
 
 # nf-core schema lint
 @schema.command()
-@click.argument("schema_path", type=click.Path(exists=True), default="nextflow_schema.json", metavar="<pipeline schema>")
+@click.argument(
+    "schema_path", type=click.Path(exists=True), default="nextflow_schema.json", metavar="<pipeline schema>"
+)
 def lint(schema_path):
     """
     Check that a given pipeline schema is valid.

nf_core/modules/lint/main_nf.py

@@ -257,9 +257,26 @@ def check_process_section(self, lines, fix_version, progress_bar):
         self.warned.append(("process_standard_label", "Process label unspecified", self.main_nf))
     for i, l in enumerate(lines):
         url = None
-        if _container_type(l) == "bioconda":
-            bioconda_packages = [b for b in l.split() if "bioconda::" in b]
         l = l.strip(" '\"")
+        if _container_type(l) == "conda":
+            bioconda_packages = [b for b in l.split() if "bioconda::" in b]
+            match = re.search(r"params\.enable_conda", l)
+            if match is None:
+                self.passed.append(
+                    (
+                        "deprecated_enable_conda",
+                        f"Deprecated parameter 'params.enable_conda' correctly not found in the conda definition",
+                        self.main_nf,
+                    )
+                )
+            else:
+                self.failed.append(
+                    (
+                        "deprecated_enable_conda",
+                        f"Found deprecated parameter 'params.enable_conda' in the conda definition",
+                        self.main_nf,
+                    )
+                )
         if _container_type(l) == "singularity":
             # e.g. "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :" -> v1.2.0_cv1
             # e.g. "https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' :" -> 0.11.9--0
@@ -471,7 +488,7 @@ def _fix_module_version(self, current_version, latest_version, singularity_tag,
     for line in lines:
         l = line.strip(" '\"")
         build_type = _container_type(l)
-        if build_type == "bioconda":
+        if build_type == "conda":
             new_lines.append(re.sub(rf"{current_version}", f"{latest_version}", line))
         elif build_type in ("singularity", "docker"):
             # Check that the new url is valid
@@ -516,8 +533,8 @@ def _get_build(response):
 
 def _container_type(line):
     """Returns the container type of a build."""
-    if re.search("bioconda::", line):
-        return "bioconda"
+    if line.startswith("conda"):
+        return "conda"
     if line.startswith("https://containers") or line.startswith("https://depot"):
         # Look for a http download URL.
         # Thanks Stack Overflow for the regex: https://stackoverflow.com/a/3809435/713980

tests/modules/lint.py

@@ -66,7 +66,7 @@ def test_modules_lint_gitlab_modules(self):
     self.mods_install_gitlab.install("multiqc")
     module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir, remote_url=GITLAB_URL)
     module_lint.lint(print_results=False, all_modules=True)
-    assert len(module_lint.failed) == 0
+    assert len(module_lint.failed) == 2
     assert len(module_lint.passed) > 0
     assert len(module_lint.warned) >= 0
 
@@ -77,7 +77,7 @@ def test_modules_lint_multiple_remotes(self):
     self.mods_install_gitlab.install("multiqc")
     module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir, remote_url=GITLAB_URL)
     module_lint.lint(print_results=False, all_modules=True)
-    assert len(module_lint.failed) == 0
+    assert len(module_lint.failed) == 1
     assert len(module_lint.passed) > 0
     assert len(module_lint.warned) >= 0
 
@@ -103,6 +103,6 @@ def test_modules_lint_patched_modules(self):
             all_modules=True,
         )
 
-    assert len(module_lint.failed) == 0
+    assert len(module_lint.failed) == 1
     assert len(module_lint.passed) > 0
     assert len(module_lint.warned) >= 0