Merge branch 'dev' into update/mqc1.31

mashehu · web-flow · commit b1e401cff41a · 2025-10-01T11:02:22.000+02:00
diff --git a/.github/snapshots/adaptivecard.nf.test.snap b/.github/snapshots/adaptivecard.nf.test.snap
@@ -106,7 +106,7 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
+            "nf-test": "0.9.3",
             "nextflow": "25.03.1"
         },
         "timestamp": "2025-05-07T13:52:10.350817122"
diff --git a/.github/snapshots/changelog.nf.test.snap b/.github/snapshots/changelog.nf.test.snap
@@ -106,7 +106,7 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
+            "nf-test": "0.9.3",
             "nextflow": "25.03.1"
         },
         "timestamp": "2025-05-07T13:52:01.993722854"
diff --git a/.github/snapshots/ci.nf.test.snap b/.github/snapshots/ci.nf.test.snap
@@ -106,7 +106,7 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
+            "nf-test": "0.9.3",
             "nextflow": "25.03.1"
         },
         "timestamp": "2025-05-07T13:52:03.306256217"
diff --git a/.github/snapshots/citations.nf.test.snap b/.github/snapshots/citations.nf.test.snap
@@ -106,7 +106,7 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
+            "nf-test": "0.9.3",
             "nextflow": "25.03.1"
         },
         "timestamp": "2025-05-07T13:52:14.716393995"
diff --git a/.github/snapshots/code_linters.nf.test.snap b/.github/snapshots/code_linters.nf.test.snap
@@ -106,7 +106,7 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
+            "nf-test": "0.9.3",
             "nextflow": "25.03.1"
         },
         "timestamp": "2025-05-07T13:52:14.716393995"
diff --git a/.github/snapshots/codespaces.nf.test.snap b/.github/snapshots/codespaces.nf.test.snap
@@ -106,7 +106,7 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
+            "nf-test": "0.9.3",
             "nextflow": "25.03.1"
         },
         "timestamp": "2025-05-07T13:52:14.716393995"
diff --git a/.github/snapshots/default.nf.test.snap b/.github/snapshots/default.nf.test.snap
@@ -106,7 +106,7 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
+            "nf-test": "0.9.3",
             "nextflow": "25.04.0"
         },
         "timestamp": "2025-05-07T13:29:04.284923"
diff --git a/.github/snapshots/documentation.nf.test.snap b/.github/snapshots/documentation.nf.test.snap
@@ -106,7 +106,7 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
+            "nf-test": "0.9.3",
             "nextflow": "25.03.1"
         },
         "timestamp": "2025-05-07T13:52:10.350817122"
diff --git a/.github/snapshots/email.nf.test.snap b/.github/snapshots/email.nf.test.snap
@@ -106,7 +106,7 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
+            "nf-test": "0.9.3",
             "nextflow": "25.03.1"
         },
         "timestamp": "2025-05-07T13:52:10.350817122"
diff --git a/.github/snapshots/fastqc.nf.test.snap b/.github/snapshots/fastqc.nf.test.snap
@@ -25,7 +25,7 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
+            "nf-test": "0.9.3",
             "nextflow": "25.03.1"
         },
         "timestamp": "2025-05-07T13:51:48.3930543"
diff --git a/.github/snapshots/github_badges.nf.test.snap b/.github/snapshots/github_badges.nf.test.snap
@@ -106,7 +106,7 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
+            "nf-test": "0.9.3",
             "nextflow": "25.03.1"
         },
         "timestamp": "2025-05-07T13:52:09.233336075"
diff --git a/.github/snapshots/gitpod.nf.test.snap b/.github/snapshots/gitpod.nf.test.snap
@@ -106,7 +106,7 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
+            "nf-test": "0.9.3",
             "nextflow": "25.03.1"
         },
         "timestamp": "2025-05-07T13:52:14.716393995"
diff --git a/.github/snapshots/gpu.nf.test.snap b/.github/snapshots/gpu.nf.test.snap
@@ -106,7 +106,7 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
+            "nf-test": "0.9.3",
             "nextflow": "25.04.0"
         },
         "timestamp": "2025-06-16T14:29:10.076573"
diff --git a/.github/snapshots/igenomes.nf.test.snap b/.github/snapshots/igenomes.nf.test.snap
@@ -106,7 +106,7 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
+            "nf-test": "0.9.3",
             "nextflow": "25.03.1"
         },
         "timestamp": "2025-05-07T13:52:07.123394148"
diff --git a/.github/snapshots/license.nf.test.snap b/.github/snapshots/license.nf.test.snap
@@ -106,7 +106,7 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
+            "nf-test": "0.9.3",
             "nextflow": "25.03.1"
         },
         "timestamp": "2025-05-07T13:52:10.350817122"
diff --git a/.github/snapshots/modules.nf.test.snap b/.github/snapshots/modules.nf.test.snap
@@ -10,7 +10,7 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
+            "nf-test": "0.9.3",
             "nextflow": "25.03.1"
         },
         "timestamp": "2025-05-07T13:51:26.771349539"
diff --git a/.github/snapshots/multiqc.nf.test.snap b/.github/snapshots/multiqc.nf.test.snap
@@ -24,7 +24,7 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
+            "nf-test": "0.9.3",
             "nextflow": "25.03.1"
         },
         "timestamp": "2025-05-07T13:51:49.209676384"
diff --git a/.github/snapshots/nf_core_configs.nf.test.snap b/.github/snapshots/nf_core_configs.nf.test.snap
@@ -106,7 +106,7 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
+            "nf-test": "0.9.3",
             "nextflow": "25.03.1"
         },
         "timestamp": "2025-05-07T13:52:14.716393995"
diff --git a/.github/snapshots/nf_schema.nf.test.snap b/.github/snapshots/nf_schema.nf.test.snap
@@ -106,7 +106,7 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
+            "nf-test": "0.9.3",
             "nextflow": "25.03.1"
         },
         "timestamp": "2025-05-07T13:52:19.694086325"
diff --git a/.github/snapshots/rocrate.nf.test.snap b/.github/snapshots/rocrate.nf.test.snap
@@ -106,9 +106,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
+            "nf-test": "0.9.3",
             "nextflow": "25.03.1"
         },
         "timestamp": "2025-05-07T13:52:10.350817122"
     }
-}
+}
diff --git a/.github/snapshots/seqera_platform.nf.test.snap b/.github/snapshots/seqera_platform.nf.test.snap
@@ -106,7 +106,7 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
+            "nf-test": "0.9.3",
             "nextflow": "25.03.1"
         },
         "timestamp": "2025-05-07T13:52:10.350817122"
diff --git a/.github/snapshots/slackreport.nf.test.snap b/.github/snapshots/slackreport.nf.test.snap
@@ -106,7 +106,7 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
+            "nf-test": "0.9.3",
             "nextflow": "25.03.1"
         },
         "timestamp": "2025-05-07T13:52:10.350817122"
diff --git a/.github/snapshots/vscode.nf.test.snap b/.github/snapshots/vscode.nf.test.snap
@@ -106,7 +106,7 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
+            "nf-test": "0.9.3",
             "nextflow": "25.03.1"
         },
         "timestamp": "2025-05-07T13:52:10.350817122"
diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
@@ -76,7 +76,7 @@ jobs:
       - name: Install nf-test
         uses: nf-core/setup-nf-test@v1
         with:
-          version: "0.9.2"
+          version: "0.9.3"
           install-pdiff: true
 
       # Create template files
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
@@ -62,7 +62,7 @@ jobs:
       - name: Install nf-test
         uses: nf-core/setup-nf-test@v1
         with:
-          version: "0.9.2"
+          version: "0.9.3"
           install-pdiff: true
 
       - name: Run nf-core/tools to create pipeline
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,11 +10,14 @@
 - Explicitly declare conda-forge as a channel in the conda setup for GitHub CI for nf-test ([#3764](https://github.com/nf-core/tools/pull/3764))
 - Update multiqc to 1.31 ([#3766](https://github.com/nf-core/tools/pull/3766))
 - Update charliecloud URL ([#3757](https://github.com/nf-core/tools/pull/3757))
+- Fix: Add NXF_VERSION environment variable to nf-test workflow ([#3770](https://github.com/nf-core/tools/pull/3770))
+- Update nf-test to 0.9.3 ([#3781](https://github.com/nf-core/tools/pull/3781))
 
 ### Linting
 
 - ignore files in gitignore also for pipeline_if_empty_null lint test ([#3722](https://github.com/nf-core/tools/pull/3722))
 - do not check pytest_modules.yml file, deprecating ([#3748](https://github.com/nf-core/tools/pull/3748))
+- Use the org from the .nf-core.yml when linting manifest name and homePage. ([#3767](https://github.com/nf-core/tools/pull/3767))
 
 ### Modules
 
@@ -23,6 +26,8 @@
 
 ### Subworkflows
 
+- Linting of patched subworkflows ([#3755](https://github.com/nf-core/tools/pull/3755))
+
 ### General
 
 - don't read param expressions with spaces as params ([#3674](https://github.com/nf-core/tools/pull/3674))
@@ -48,6 +53,7 @@
 - Fix backwards compatibility with python 3.9 in use of Enum ([#3736](https://github.com/nf-core/tools/pull/3736))
 - Fix downloads: temporary files not moved and cleaned up correctly after singularity pull ([#3749](https://github.com/nf-core/tools/pull/3749))
 - impr devcontainer: Add hostRequirements to run with 4CPUs and 16GB ram by default ([#3746](https://github.com/nf-core/tools/pull/3746))
+- Add .nf-test/ to prettier ignore list ([#3776](https://github.com/nf-core/tools/pull/3776))
 
 ## [v3.3.2 - Tungsten Tamarin Patch 2](https://github.com/nf-core/tools/releases/tag/3.3.2) - [2025-07-08]
 
diff --git a/nf_core/components/components_test.py b/nf_core/components/components_test.py
@@ -208,13 +208,12 @@ def generate_snapshot(self) -> bool:
             obsolete_snapshots = compiled_pattern.search(nftest_out.decode())
             if obsolete_snapshots:
                 self.obsolete_snapshots = True
-
             # check if nf-test was successful
             if "Assertion failed:" in nftest_out.decode():
                 return False
-            elif "no valid tests found." in nftest_out.decode():
-                log.error("Test file 'main.nf.test' not found")
-                self.errors.append("Test file 'main.nf.test' not found")
+            elif "No tests to execute." in nftest_out.decode():
+                log.error("Nothing to execute. Is the file 'main.nf.test' missing?")
+                self.errors.append("Nothing to execute. Is the file 'main.nf.test' missing?")
                 return False
             else:
                 log.debug("nf-test successful")
diff --git a/nf_core/components/info.py b/nf_core/components/info.py
@@ -165,7 +165,7 @@ def get_component_info(self):
             self.meta = self.get_remote_yaml()
 
         # Could not find the meta
-        if self.meta is False:
+        if self.meta is None:
             raise UserWarning(f"Could not find {self.component_type[:-1]} '{self.component}'")
 
         return self.generate_component_info_help()
diff --git a/nf_core/pipeline-template/.github/workflows/nf-test.yml b/nf_core/pipeline-template/.github/workflows/nf-test.yml
@@ -18,7 +18,7 @@ concurrency:
 
 env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-  NFT_VER: "0.9.2"
+  NFT_VER: "0.9.3"
   NFT_WORKDIR: "~"
   NXF_ANSI_LOG: false
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
@@ -97,6 +97,7 @@ jobs:
         continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }}
         env:
           NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
+          NXF_VERSION: ${{ matrix.NXF_VER }}
         with:
           profile: ${{ matrix.profile }}
           shard: ${{ matrix.shard }}
diff --git a/nf_core/pipeline-template/.prettierignore b/nf_core/pipeline-template/.prettierignore
@@ -16,6 +16,7 @@ testing/
 testing*
 *.pyc
 bin/
+.nf-test/
 {%- if rocrate %}
 ro-crate-metadata.json
 {%- endif %}
diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py
@@ -5,6 +5,7 @@
 from typing import Optional, Union
 
 from nf_core.pipelines.schema import PipelineSchema
+from nf_core.utils import load_tools_config
 
 log = logging.getLogger(__name__)
 
@@ -255,30 +256,35 @@ def nextflow_config(self) -> dict[str, list[str]]:
         else:
             failed.append(f"Config ``{k}`` did not have correct value: ``{self.nf_config.get(k)}``")
 
+    _, nf_core_yaml_config = load_tools_config(self.wf_path)
+    org_name = "nf-core"
+    if nf_core_yaml_config and getattr(nf_core_yaml_config, "template", None):
+        org_name = getattr(nf_core_yaml_config.template, "org", org_name) or org_name
+
     if "manifest.name" not in ignore_configs:
         # Check that the pipeline name starts with nf-core
         try:
             manifest_name = self.nf_config.get("manifest.name", "").strip("'\"")
-            if not manifest_name.startswith("nf-core/"):
+            if not manifest_name.startswith(f"{org_name}/"):
                 raise AssertionError()
         except (AssertionError, IndexError):
-            failed.append(f"Config ``manifest.name`` did not begin with ``nf-core/``:\n    {manifest_name}")
+            failed.append(f"Config ``manifest.name`` did not begin with ``{org_name}/``:\n    {manifest_name}")
         else:
-            passed.append("Config ``manifest.name`` began with ``nf-core/``")
+            passed.append(f"Config ``manifest.name`` began with ``{org_name}/``")
 
     if "manifest.homePage" not in ignore_configs:
         # Check that the homePage is set to the GitHub URL
         try:
             manifest_homepage = self.nf_config.get("manifest.homePage", "").strip("'\"")
-            if not manifest_homepage.startswith("https://github.com/nf-core/"):
+            if not manifest_homepage.startswith(f"https://github.com/{org_name}/"):
                 raise AssertionError()
         except (AssertionError, IndexError):
             failed.append(
-                f"Config variable ``manifest.homePage`` did not begin with https://github.com/nf-core/:\n    {manifest_homepage}"
+                f"Config variable ``manifest.homePage`` did not begin with https://github.com/{org_name}/:\n    {manifest_homepage}"
             )
 
         else:
-            passed.append("Config variable ``manifest.homePage`` began with https://github.com/nf-core/")
+            passed.append(f"Config variable ``manifest.homePage`` began with https://github.com/{org_name}/")
 
     # Check that the DAG filename ends in ``.svg``
     if "dag.file" in self.nf_config:
diff --git a/nf_core/subworkflows/lint/subworkflow_changes.py b/nf_core/subworkflows/lint/subworkflow_changes.py
@@ -42,7 +42,13 @@ def subworkflow_changes(subworkflow_lint_object, subworkflow):
                 with open(tempdir / file, "w") as fh:
                     fh.writelines(lines)
         except LookupError:
-            # This error is already reported by subworkflow_patch, so just return
+            subworkflow.failed.append(
+                (
+                    "subworkflow_patch",
+                    "Subworkflow patch cannot be cleanly applied",
+                    f"{subworkflow.component_dir}",
+                )
+            )
             return
     else:
         tempdir = subworkflow.component_dir
diff --git a/tests/components/test_components_generate_snapshot.py b/tests/components/test_components_generate_snapshot.py
@@ -136,5 +136,5 @@ def test_test_not_found(self):
             test_file.rename(test_file.parent / "main.nf.test.bak")
             with pytest.raises(UserWarning) as e:
                 snap_generator.run()
-            assert "Test file 'main.nf.test' not found" in str(e.value)
+            assert "Nothing to execute. Is the file 'main.nf.test' missing?" in str(e.value)
             Path(test_file.parent / "main.nf.test.bak").rename(test_file)
diff --git a/tests/subworkflows/test_lint.py b/tests/subworkflows/test_lint.py
diff --git a/tests/subworkflows/test_patch.py b/tests/subworkflows/test_patch.py

Original file line number	Diff line number	Diff line change
`@@ -106,7 +106,7 @@`
`106`	`106`	`]`
`107`	`107`	`],`
`108`	`108`	`"meta": {`
`109`		`- "nf-test": "0.9.2",`
	`109`	`+ "nf-test": "0.9.3",`
`110`	`110`	`"nextflow": "25.03.1"`
`111`	`111`	`},`
`112`	`112`	`"timestamp": "2025-05-07T13:52:10.350817122"`
Original file line number	Diff line number	Diff line change
`@@ -25,7 +25,7 @@`
`25`	`25`	`]`
`26`	`26`	`],`
`27`	`27`	`"meta": {`
`28`		`- "nf-test": "0.9.2",`
	`28`	`+ "nf-test": "0.9.3",`
`29`	`29`	`"nextflow": "25.03.1"`
`30`	`30`	`},`
`31`	`31`	`"timestamp": "2025-05-07T13:51:48.3930543"`