nf-core · mashehu · Oct 1, 2025 · Sep 30, 2025 · Sep 30, 2025 · Sep 30, 2025
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
@@ -10,6 +10,7 @@
 - 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 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
 

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/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

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)