Merge pull request #70 from gagnonanthony/synthbeterror

#40 - Catch exit code error for `betcrop/synthstrip` + stub run test
scilus · Dec 19, 2024 · fb6f35a · fb6f35a
2 parents 81ec899 + 3c29e13
commit fb6f35a
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Showing 3 changed files with 56 additions and 6 deletions.
diff --git a/modules/nf-neuro/betcrop/synthbet/main.nf b/modules/nf-neuro/betcrop/synthbet/main.nf
@@ -40,14 +40,21 @@ process BETCROP_SYNTHBET {
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
-    mri_synthstrip -h
-
     touch ${prefix}__bet_image.nii.gz
     touch ${prefix}__brain_mask.nii.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         Freesurfer: \$(mri_convert -version | grep "freesurfer" | sed -E 's/.* ([0-9]+\\.[0-9]+\\.[0-9]+).*/\\1/')
     END_VERSIONS
+
+    function handle_code () {
+    local code=\$?
+    ignore=( 1 )
+    exit \$([[ " \${ignore[@]} " =~ " \$code " ]] && echo 0 || echo \$code)
+    }
+    trap 'handle_code' ERR
+
+    mri_synthstrip -h
     """
 }
diff --git a/modules/nf-neuro/betcrop/synthbet/tests/main.nf.test b/modules/nf-neuro/betcrop/synthbet/tests/main.nf.test
@@ -14,7 +14,6 @@ nextflow_process {
     tag "subworkflows/load_test_data"
 
     test("betcrop - synthbet") {
-
         setup {
             run("LOAD_TEST_DATA", alias: "LOAD_DATA") {
                 script "../../../../../subworkflows/nf-neuro/load_test_data/main.nf"
@@ -26,7 +25,6 @@ nextflow_process {
                 }
             }
         }
-
         when {
             process {
                 """
@@ -40,12 +38,45 @@ nextflow_process {
                 """
             }
         }
-
         then {
             assertAll(
                 { assert process.success },
                 { assert snapshot(process.out).match() }
             )
         }
     }
+
+    test("betcrop - synthbet - stub-run") {
+        options "-stub-run"
+        setup {
+            run("LOAD_TEST_DATA", alias: "LOAD_DATA") {
+                script "../../../../../subworkflows/nf-neuro/load_test_data/main.nf"
+                process {
+                    """
+                    input[0] = Channel.from( [ "freesurfer.zip" ] )
+                    input[1] = "test.load-test-data"
+                    """
+                }
+            }
+        }
+        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}/anat_image.nii.gz"),
+                        []
+                    ]
+                }
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match() }
+            )
+        }
+    }
 }
diff --git a/modules/nf-neuro/betcrop/synthbet/tests/main.nf.test.snap b/modules/nf-neuro/betcrop/synthbet/tests/main.nf.test.snap
@@ -1,4 +1,16 @@
 {
+    "betcrop - synthbet - stub-run": {
+        "content": [
+            [
+                "versions.yml:md5,c639461870ca534b5105f61d672f740f"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-12-12T10:54:37.644838"
+    },
     "betcrop - synthbet": {
         "content": [
             {
@@ -52,4 +64,4 @@
         },
         "timestamp": "2024-11-25T18:19:01.459548926"
     }
-}
+}