From 6704412d1a035151a43104dfa987dc5b09ae05b5 Mon Sep 17 00:00:00 2001
From: Thoumyre Stanislas <stanislasth@outlook.fr>
Date: Thu, 31 Oct 2024 15:49:09 +0000
Subject: [PATCH] add test eddy full

---
 .../nf-neuro/preproc/eddy/tests/main.nf.test  | 44 +++++++++++++++++--
 .../preproc/eddy/tests/main.nf.test.snap      | 32 ++++++++++++++
 2 files changed, 73 insertions(+), 3 deletions(-)

diff --git a/modules/nf-neuro/preproc/eddy/tests/main.nf.test b/modules/nf-neuro/preproc/eddy/tests/main.nf.test
index 61ce4ad..a4812a7 100644
--- a/modules/nf-neuro/preproc/eddy/tests/main.nf.test
+++ b/modules/nf-neuro/preproc/eddy/tests/main.nf.test
@@ -19,14 +19,14 @@ nextflow_process {
                 script "../../../../../subworkflows/nf-neuro/load_test_data/main.nf"
                 process {
                     """
-                    input[0] = Channel.from( [ "raw_DWIss1000-dir32.zip", "TOPUP.zip" ] )
+                    input[0] = Channel.from( [ "raw_DWIss1000-dir32.zip", "TOPUP.zip", "topup_eddy_light.zip" ] )
                     input[1] = "test.load-test-data"
                     """
                 }
             }
         }
 
-    test("eddy") {
+    test("eddy_light") {
         when {
             process {
                 """
@@ -34,6 +34,7 @@ nextflow_process {
                     .branch{
                         raw_dwi: it.simpleName == "raw_DWIss1000-dir32"
                         topup_results: it.SimpleName == "TOPUP"
+                        rev_dwi: it.simpleName == "topup_eddy_light.zip"
                     }
                 ch_raw_dwi = ch_split_test_data.raw_dwi
                     .map{ test_data_directory -> [
@@ -50,12 +51,49 @@ nextflow_process {
                         file("\${test_data_directory}/topup_corrected_b0s.nii.gz", checkIfExists: true),
                         file("\${test_data_directory}/topup_fieldcoef.nii.gz", checkIfExists: true),
                         file("\${test_data_directory}/topup_movpar.txt", checkIfExists: true)]}
-
                 input[0] = ch_raw_dwi.join(ch_topup)
                 """
             }
         }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.dwi_corrected.get(0).get(1)).name,
+                    process.out.bval_corrected,
+                    file(process.out.bvec_corrected.get(0).get(1)).name,
+                    process.out.b0_mask,
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
 
+    test("eddy_full") {
+        when {
+            process {
+                """
+                ch_split_test_data = LOAD_DATA.out.test_data_directory
+                    .branch{
+                        raw_dwi: it.simpleName == "raw_DWIss1000-dir32"
+                        topup_results: it.SimpleName == "TOPUP"
+                        rev_dwi: it.simpleName == "topup_eddy_light.zip"
+                    }
+                input[0] = ch_split_test_data.rev_dwi
+                    .map{ test_data_directory -> [
+                    [ id:'test', single_end:false ], // meta map
+                    file("\${test_data_directory}/sub-01_dir-AP_dwi.nii.gz", checkIfExists: true),
+                    file("\${test_data_directory}/sub-01_dir-AP_dwi.bval", checkIfExists: true),
+                    file("\${test_data_directory}/sub-01_dir-AP_dwi.bvec", checkIfExists: true),
+                    file("\${test_data_directory}/sub-01_dir-PA_dwi.nii.gz", checkIfExists: true),
+                    file("\${test_data_directory}/sub-01_dir-PA_dwi.bval", checkIfExists: true),
+                    file("\${test_data_directory}/sub-01_dir-PA_dwi.bvec", checkIfExists: true),
+                    file("\${test_data_directory}/sub-01__corrected_b0s.nii.gz", checkIfExists: true),
+                    file("\${test_data_directory}/topup_results_fieldcoef.nii.gz", checkIfExists: true),
+                    file("\${test_data_directory}/topup_results_movpar.txt", checkIfExists: true)]}
+                    """
+            }
+        }
         then {
             assertAll(
                 { assert process.success },
diff --git a/modules/nf-neuro/preproc/eddy/tests/main.nf.test.snap b/modules/nf-neuro/preproc/eddy/tests/main.nf.test.snap
index 61a68cb..e267aec 100644
--- a/modules/nf-neuro/preproc/eddy/tests/main.nf.test.snap
+++ b/modules/nf-neuro/preproc/eddy/tests/main.nf.test.snap
@@ -1,4 +1,36 @@
 {
+    "eddy_light": {
+        "content": [
+            "test__dwi_corrected.nii.gz",
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test__bval_eddy:md5,7995daabbd74fcf7c365a39a779f67e9"
+                ]
+            ],
+            "test__dwi_eddy_corrected.bvec",
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test__b0_bet_mask.nii.gz:md5,2dd16e0c664c910f1970b96056866fea"
+                ]
+            ],
+            [
+                "versions.yml:md5,137e3ce0fd25e5b16de2d8cc5a5aefca"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-31T13:17:58.524376706"
+    },
     "eddy": {
         "content": [
             "test__dwi_corrected.nii.gz",