Merge pull request #69 from gagnonanthony/betcatcherror

#40 - Catch exit code in stub of `betcrop/fslbetcrop`
scilus · Dec 18, 2024 · 68cde77 · 68cde77
2 parents 8702891 + 4314d85
commit 68cde77
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Showing 3 changed files with 53 additions and 7 deletions.
diff --git a/modules/nf-neuro/betcrop/fslbetcrop/main.nf b/modules/nf-neuro/betcrop/fslbetcrop/main.nf
@@ -69,16 +69,9 @@ process BETCROP_FSLBETCROP {
     """
 
     stub:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
-    scil_dwi_extract_b0.py -h
-    bet -h
-    scil_volume_math.py -h
-    mrcalc -h
-    scil_volume_crop.py -h
-
     touch ${prefix}__image_bet.nii.gz
     touch ${prefix}__image_bet_mask.nii.gz
     touch ${prefix}__image_boundingBox.pkl
@@ -89,5 +82,18 @@ process BETCROP_FSLBETCROP {
         mrtrix: \$(mrcalc -version 2>&1 | sed -n 's/== mrcalc \\([0-9.]\\+\\).*/\\1/p')
         fsl: \$(flirt -version 2>&1 | sed -n 's/FLIRT version \\([0-9.]\\+\\)/\\1/p')
     END_VERSIONS
+
+    function handle_code () {
+    local code=\$?
+    ignore=( 1 )
+    exit \$([[ " \${ignore[@]} " =~ " \$code " ]] && echo 0 || echo \$code)
+    }
+    trap 'handle_code' ERR
+
+    bet
+    scil_dwi_extract_b0.py -h
+    scil_volume_math.py -h
+    mrcalc -h
+    scil_volume_crop.py -h
     """
 }
diff --git a/modules/nf-neuro/betcrop/fslbetcrop/tests/main.nf.test b/modules/nf-neuro/betcrop/fslbetcrop/tests/main.nf.test
@@ -108,4 +108,32 @@ nextflow_process {
 
     }
 
+    test("betcrop - fslbetcrop - stub-run") {
+
+        options "-stub-run"
+
+        when {
+            process {
+                """
+                input[0] = LOAD_DATA.out.test_data_directory.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ], // meta map
+                        file("\${test_data_directory}/dwi/dwi.nii.gz"),
+                        file("\${test_data_directory}/dwi/dwi.bval"),
+                        file("\${test_data_directory}/dwi/dwi.bvec")
+                    ]
+                }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match() }
+            )
+        }
+
+    }
+
 }
diff --git a/modules/nf-neuro/betcrop/fslbetcrop/tests/main.nf.test.snap b/modules/nf-neuro/betcrop/fslbetcrop/tests/main.nf.test.snap
@@ -1,4 +1,16 @@
 {
+    "betcrop - fslbetcrop - stub-run": {
+        "content": [
+            [
+                "versions.yml:md5,cc45ab23921525536874337c1c88e5cf"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-12-12T10:33:04.50811"
+    },
     "betcrop - fslbetcrop - dwi": {
         "content": [
             {