[FIX] separate freesurfer-related process testing to a separate actio…

…n run to avoid memory issues
scilus · Nov 19, 2024 · 45ee20c · 45ee20c
1 parent 8ea6bd5
commit 45ee20c
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Showing 3 changed files with 34 additions and 51 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -35,7 +35,8 @@ jobs:
           - "docker"
           - "singularity"
         test_name:
-          - "test"
+          - "main.nf.test"
+          - "freesurfer.nf.test"
         isMaster:
           - ${{ github.base_ref == 'master' }}
         # Exclude conda and singularity on dev
@@ -76,4 +77,4 @@ jobs:
 
       - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
         run: |
-          nf-test test ${GITHUB_WORKSPACE} --profile ${{ matrix.profile }}
+          nf-test test ${GITHUB_WORKSPACE}/tests/${{ matrix.test_name }} --profile ${{ matrix.profile }}
diff --git a/tests/freesurfer.nf.test b/tests/freesurfer.nf.test
@@ -0,0 +1,29 @@
+nextflow_pipeline {
+
+    options "-stub-run"
+
+    name "Test nf-pediatric freesurfer workflows main.nf"
+    script "../main.nf"
+
+    test("Freesurfer profile - should run successfully") {
+
+        when {
+            params {
+
+                params.input = "$projectDir/tests/data/samplesheet_testtracking.csv"
+                params.outdir = "test_results/"
+
+                params.freesurfer = true
+                params.fs_license = "https://www.dropbox.com/scl/fi/0s8lp6lydyd0rxawxb4jm/license.txt?rlkey=hz54oc0d4sor69avqphtrjvgn&st=9e0yij97&dl=0"
+
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert workflow.trace.tasks().size() == 3
+        }
+
+    }
+
+}
diff --git a/tests/main.nf.test b/tests/main.nf.test
@@ -271,61 +271,16 @@ nextflow_pipeline {
 
     }
 
-    test("Freesurfer profile - should run successfully") {
+    test("Connectomics + tracking profiles - should run successfully") {
 
         when {
             params {
 
                 params.input = "$projectDir/tests/data/samplesheet_testtracking.csv"
                 params.outdir = "test_results/"
 
-                params.freesurfer = true
-                params.fs_license = "https://www.dropbox.com/scl/fi/0s8lp6lydyd0rxawxb4jm/license.txt?rlkey=hz54oc0d4sor69avqphtrjvgn&st=9e0yij97&dl=0"
-
-            }
-        }
-
-        then {
-            assert workflow.success
-            assert workflow.trace.tasks().size() == 3
-        }
-
-    }
-
-    test("Freesurfer + connectomics profiles - should run successfully") {
-
-        when {
-            params {
-
-                params.input = "$projectDir/tests/data/samplesheet_testconn.csv"
-                params.outdir = "test_results/"
-
-                params.freesurfer = true
-                params.connectomics = true
-                params.fs_license = "https://www.dropbox.com/scl/fi/0s8lp6lydyd0rxawxb4jm/license.txt?rlkey=hz54oc0d4sor69avqphtrjvgn&st=9e0yij97&dl=0"
-
-            }
-        }
-
-        then {
-            assert workflow.success
-            assert workflow.trace.tasks().size() == 9
-        }
-
-    }
-
-    test("Freesurfer + connectomics + tracking profiles - should run successfully") {
-
-        when {
-            params {
-
-                params.input = "$projectDir/tests/data/samplesheet_testtracking.csv"
-                params.outdir = "test_results/"
-
-                params.freesurfer = true
                 params.connectomics = true
                 params.tracking = true
-                params.fs_license = "https://www.dropbox.com/scl/fi/0s8lp6lydyd0rxawxb4jm/license.txt?rlkey=hz54oc0d4sor69avqphtrjvgn&st=9e0yij97&dl=0"
 
             }
         }
@@ -337,18 +292,16 @@ nextflow_pipeline {
 
     }
 
-    test("Freesurfer + connectomics + tracking profiles with additional metrics - should run successfully") {
+    test("Connectomics + tracking profiles with additional metrics - should run successfully") {
 
         when {
             params {
 
                 params.input = "$projectDir/tests/data/samplesheet_testtracking_withmetrics.csv"
                 params.outdir = "test_results/"
 
-                params.freesurfer = true
                 params.connectomics = true
                 params.tracking = true
-                params.fs_license = "https://www.dropbox.com/scl/fi/0s8lp6lydyd0rxawxb4jm/license.txt?rlkey=hz54oc0d4sor69avqphtrjvgn&st=9e0yij97&dl=0"
 
             }
         }