Merge branch 'dev' into fresh-nf-test

.github/workflows/ci.yml

@@ -95,12 +95,10 @@ jobs:
           path: ~/.cache/pip
           key: ${{ runner.os }}-pip-pdiff
 
-      - name: Set up pdiff to see diff between nf-test snapshots
-        run: |
-          python -m pip install --upgrade pip
-          pip install pdiff cryptography
+      - name: Install pdiff
+        run: python -m pip install --upgrade pip pdiff cryptography
 
-      - name: Set up Miniconda
+      - name: Set up miniconda
         if: matrix.profile == 'conda'
         uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3
         with:

nf-test.config

@@ -1,10 +1,18 @@
 config {
+    // location for all nf-tests
     testsDir "."
-    workDir ".nf-test"
+
+    // nf-test directory including temporary files for each test
+    workDir System.getenv("NFT_WORKDIR") ?: ".nf-test"
+
+    // location of an optional nextflow.config file specific for executing tests
     configFile "conf/test.config"
+
+    // run all test with defined profile(s) from the main nextflow.config
     profile "test"
     triggers 'nextflow.config', 'nf-test.config', 'conf/test.config', 'conf/test_full.config'
 
+    // Include plugins
     plugins {
         load "[email protected]"
         load "[email protected]"

tests/default.nf.test

@@ -2,6 +2,8 @@ nextflow_pipeline {
 
     name "Test pipeline"
     script "../main.nf"
+    tag "pipeline"
+    tag "pipeline_sarek"
 
     test("Run with profile test") {
 
@@ -50,7 +52,7 @@ nextflow_pipeline {
         then {
             assertAll(
                 { assert workflow.failed},
-                { assert workflow.stderr.contains("* -- Entry 2 - sample: Sample ID must be provided and cannot contain spaces (test 2)") }
+                { assert workflow.stderr.toString().contains("Sample ID must be provided and cannot contain spaces") }
             )
         }
     }

tests/default.nf.test.snap

@@ -324,4 +324,4 @@
         },
         "timestamp": "2024-10-08T12:09:25.505363"
     }
-}
+}