#40 - Catch errors in stub for fastseg, fsreconall, and fastsurfer + add stub tests

modules/nf-neuro/registration/synthregistration/main.nf

@@ -3,7 +3,9 @@ process REGISTRATION_SYNTHREGISTRATION {
     label 'process_high'
 
     container "freesurfer/synthmorph:3"
-    containerOptions "--entrypoint '' --env PYTHONPATH='/freesurfer/env/lib/python3.11/site-packages'"
+    containerOptions {
+        (workflow.containerEngine == 'docker') ? '--entrypoint "" --env PYTHONPATH="/freesurfer/env/lib/python3.11/site-packages"' : "--env PYTHONPATH='/freesurfer/env/lib/python3.11/site-packages'"
+    }
 
     input:
     tuple val(meta), path(moving), path(fixed)

modules/nf-neuro/segmentation/fastseg/main.nf

@@ -54,9 +54,6 @@ process SEGMENTATION_FASTSEG {
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
-    fast -h
-    scil_volume_math.py -h
-
     touch ${prefix}__mask_wm.nii.gz
     touch ${prefix}__mask_gm.nii.gz
     touch ${prefix}__mask_csf.nii.gz
@@ -69,5 +66,15 @@ process SEGMENTATION_FASTSEG {
         scilpy: 2.0.0
         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
+
+    fast -h
+    scil_volume_math.py -h
     """
 }

modules/nf-neuro/segmentation/fastseg/tests/main.nf.test

@@ -87,4 +87,27 @@ nextflow_process {
             )
         }
     }
+    test("segmentation - fastseg - 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}/T1w.nii.gz", checkIfExists: true,),
+                        []
+                    ]
+                }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match() }
+            )
+        }
+    }
 }

modules/nf-neuro/segmentation/fastseg/tests/main.nf.test.snap

@@ -34,5 +34,17 @@
             "nextflow": "24.04.4"
         },
         "timestamp": "2024-09-04T20:03:24.730234"
+    },
+    "segmentation - fastseg - stub-run": {
+        "content": [
+            [
+                "versions.yml:md5,e9c2afb5537207544dc1b54cbdc389a4"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-12-12T14:01:36.729872"
     }
 }

modules/nf-neuro/segmentation/fastsurfer/main.nf

@@ -3,24 +3,25 @@ process SEGMENTATION_FASTSURFER {
     label 'process_single'
 
     container "${ 'deepmi/fastsurfer:cpu-v2.2.0' }"
-
-    containerOptions '--entrypoint ""'
+    containerOptions {
+        (workflow.containerEngine == 'docker') ? '--entrypoint ""' : ''
+    }
 
     input:
         tuple val(meta), path(anat), path(fs_license)
 
     output:
-        tuple val(meta), path("*_fastsurfer")    , emit: fastsurferdirectory
-        path "versions.yml"                 , emit: versions
+        tuple val(meta), path("*_fastsurfer")       , emit: fastsurferdirectory
+        path "versions.yml"                         , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-        def prefix = task.ext.prefix ?: "${meta.id}"
-        def acq3T = task.ext.acq3T ? "--3T" : ""
-        def FASTSURFER_HOME = "/fastsurfer"
-        def SUBJECTS_DIR = "${prefix}_fastsurfer"
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def acq3T = task.ext.acq3T ? "--3T" : ""
+    def FASTSURFER_HOME = "/fastsurfer"
+    def SUBJECTS_DIR = "${prefix}_fastsurfer"
     """
     mkdir ${prefix}_fastsurfer/
     $FASTSURFER_HOME/run_fastsurfer.sh  --allow_root \
@@ -38,14 +39,24 @@ process SEGMENTATION_FASTSURFER {
     """
 
     stub:
-        def prefix = task.ext.prefix ?: "${meta.id}"
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def FASTSURFER_HOME = "/fastsurfer"
 
     """
-    $FASTSURFER_HOME/run_fastsurfer.sh --version
+    mkdir ${prefix}_fastsurfer/
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        fastersurfer: 2.2.0+9f37d02
+        fastersurfer: \$($FASTSURFER_HOME/run_fastsurfer.sh --version)
     END_VERSIONS
+
+    function handle_code () {
+    local code=\$?
+    ignore=( 1 )
+    exit \$([[ " \${ignore[@]} " =~ " \$code " ]] && echo 0 || echo \$code)
+    }
+    trap 'handle_code' ERR
+
+    $FASTSURFER_HOME/run_fastsurfer.sh --version
     """
 }

modules/nf-neuro/segmentation/fastsurfer/tests/main.nf.test

@@ -47,4 +47,27 @@ nextflow_process {
             )
         }
     }
+
+    test("segmentation - fastsurfer - stub-run") {
+        options "-stub-run"
+        when {
+            process {
+                """
+                input[0] = LOAD_DATA.out.test_data_directory.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
+                        file("\${test_data_directory}/anat_image.nii.gz"),
+                        file("\${test_data_directory}/license.txt")
+                    ]
+                }
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match() }
+            )
+        }
+    }
 }

modules/nf-neuro/segmentation/fastsurfer/tests/main.nf.test.snap

@@ -1,4 +1,16 @@
 {
+    "segmentation - fastsurfer - stub-run": {
+        "content": [
+            [
+                "versions.yml:md5,b263ce2ef1818492be3805ba8e49b50f"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-12-12T13:38:50.551338"
+    },
     "segmentation - fastsurfer": {
         "content": [
             "test_fastsurfer",

modules/nf-neuro/segmentation/fsreconall/main.nf

@@ -59,13 +59,20 @@ process SEGMENTATION_FSRECONALL {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    recon-all --help
-
     mkdir ${prefix}__recon_all
 
     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
+
+    recon-all --help
     """
 }

modules/nf-neuro/segmentation/fsreconall/tests/main.nf.test

@@ -80,4 +80,30 @@ nextflow_process {
 
     }
 
+    test("segmentation - fsreconall - stub-run") {
+        options "-stub-run"
+        when {
+            config "./nextflow_debug.config"
+
+            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"),
+                        file("\${test_data_directory}/license.txt")
+                    ]}
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match() }
+            )
+        }
+
+    }
+
 }

modules/nf-neuro/segmentation/fsreconall/tests/main.nf.test.snap

@@ -1,4 +1,16 @@
 {
+    "segmentation - fsreconall - stub-run": {
+        "content": [
+            [
+                "versions.yml:md5,2a7185588fa8c664d53c4c08637285e6"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-12-12T13:55:39.259005"
+    },
     "segmentation - fsreconall": {
         "content": [
             "test__recon_all",