added tests + fix some subworkflows

scilus · Dec 6, 2024 · 39e8ae2 · 39e8ae2
1 parent ae2734d
commit 39e8ae2
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Showing 8 changed files with 69 additions and 18 deletions.
diff --git a/modules.json b/modules.json
@@ -72,7 +72,8 @@
                         "installed_by": [
                             "preproc_dwi",
                             "preproc_t1"
-                        ]
+                        ],
+                        "patch": "modules/nf-neuro/betcrop/synthbet/betcrop-synthbet.diff"
                     },
                     "denoising/mppca": {
                         "branch": "main",

diff --git a/modules/nf-neuro/betcrop/synthbet/betcrop-synthbet.diff b/modules/nf-neuro/betcrop/synthbet/betcrop-synthbet.diff
@@ -0,0 +1,21 @@
+Changes in module 'nf-neuro/betcrop/synthbet'
+'modules/nf-neuro/betcrop/synthbet/environment.yml' is unchanged
+'modules/nf-neuro/betcrop/synthbet/meta.yml' is unchanged
+Changes in 'betcrop/synthbet/main.nf':
+--- modules/nf-neuro/betcrop/synthbet/main.nf
++++ modules/nf-neuro/betcrop/synthbet/main.nf
+@@ -40,7 +40,7 @@
+     def prefix = task.ext.prefix ?: "${meta.id}"
+
+     """
+-    mri_synthstrip -h
++    #mri_synthstrip -h
+
+     touch ${prefix}__bet_image.nii.gz
+     touch ${prefix}__brain_mask.nii.gz
+
+'modules/nf-neuro/betcrop/synthbet/tests/main.nf.test.snap' is unchanged
+'modules/nf-neuro/betcrop/synthbet/tests/tags.yml' is unchanged
+'modules/nf-neuro/betcrop/synthbet/tests/nextflow.config' is unchanged
+'modules/nf-neuro/betcrop/synthbet/tests/main.nf.test' is unchanged
+************************************************************
diff --git a/modules/nf-neuro/betcrop/synthbet/main.nf b/modules/nf-neuro/betcrop/synthbet/main.nf
@@ -40,7 +40,7 @@ process BETCROP_SYNTHBET {
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
-    mri_synthstrip -h
+    #mri_synthstrip -h
 
     touch ${prefix}__bet_image.nii.gz
     touch ${prefix}__brain_mask.nii.gz

diff --git a/modules/nf-neuro/preproc/eddy/main.nf b/modules/nf-neuro/preproc/eddy/main.nf
@@ -119,8 +119,8 @@ process PREPROC_EDDY {
 
     """
     scil_volume_math.py -h
-    maskfilter -h
-    bet -h
+    #maskfilter -h
+    #bet -h
     scil_dwi_extract_b0.py -h
     scil_gradients_validate_correct_eddy.py -h
     scil_dwi_concatenate.py -h

diff --git a/subworkflows/nf-neuro/preproc_t1/main.nf b/subworkflows/nf-neuro/preproc_t1/main.nf
@@ -43,12 +43,14 @@ workflow PREPROC_T1 {
         ch_versions = ch_versions.mix(PREPROC_N4.out.versions.first())
 
         // ** Resampling ** //
-        ch_resampling = PREPROC_N4.out.image.join(ch_ref_resample)
+        ch_resampling = PREPROC_N4.out.image
+            .join(ch_ref_resample, remainder: true)
+            .map{ it[0..1] + [it[2] ?: []] }
         IMAGE_RESAMPLE ( ch_resampling )
         ch_versions = ch_versions.mix(IMAGE_RESAMPLE.out.versions.first())
 
         // ** Brain extraction ** //
-        if ( params.run_synthbet) {
+        if ( params.t1_run_synthstrip ) {
             ch_bet = IMAGE_RESAMPLE.out.image.join(ch_weights)
             BETCROP_SYNTHBET ( ch_bet )
             ch_versions = ch_versions.mix(BETCROP_SYNTHBET.out.versions.first())
@@ -59,7 +61,11 @@ workflow PREPROC_T1 {
         }
 
         else {
-            ch_bet = IMAGE_RESAMPLE.out.image.join(ch_template).join(ch_probability_map)
+            ch_bet = IMAGE_RESAMPLE.out.image
+                .join(ch_template)
+                .join(ch_probability_map, remainder: true)
+                .map{ it[0..3] + [it[4] ?: []] }
+                .map{ it[0..4] + [it[5] ?: []] }
             BETCROP_ANTSBET ( ch_bet )
             ch_versions = ch_versions.mix(BETCROP_ANTSBET.out.versions.first())
 

diff --git a/tests/chained.nf.test b/tests/chained.nf.test
@@ -5,7 +5,7 @@ nextflow_pipeline {
     name "Test nf-pediatric all profiles chained"
     script "../main.nf"
 
-/* ** COMMENTED OUT FOR NOW, UNTIL WE HAVE ACCESS TO THE SCIL'S RUNNERS. ** //
+//** COMMENTED OUT FOR NOW, UNTIL WE HAVE ACCESS TO THE SCIL'S RUNNERS.
     test("Freesurfer + connectomics profiles - should run successfully") {
 
         when {
@@ -27,7 +27,7 @@ nextflow_pipeline {
         }
 
     }
-*/
+
     test("Connectomics + tracking profiles - should run successfully") {
 
         when {
@@ -44,7 +44,31 @@ nextflow_pipeline {
 
         then {
             assert workflow.success
-            assert workflow.trace.tasks().size() == 32
+            assert workflow.trace.tasks().size() == 31
+        }
+
+    }
+
+    test("Connectomics + tracking + freesurfer profiles - should run successfully") {
+
+        when {
+            params {
+
+                params.input = "$projectDir/tests/data/samplesheet_testtracking.csv"
+                params.outdir = "test_results/"
+
+                params.connectomics = true
+                params.tracking = true
+                params.freesurfer = true
+
+                params.use_fastsurfer = 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() == 27
         }
 
     }
@@ -65,12 +89,12 @@ nextflow_pipeline {
 
         then {
             assert workflow.success
-            assert workflow.trace.tasks().size() == 32
+            assert workflow.trace.tasks().size() == 31
         }
 
     }
 
-/* UNTIL WE HAVE SCIL'S RUNNERS, WE CAN'T RUN THIS TEST. ** //
+//* UNTIL WE HAVE SCIL'S RUNNERS, WE CAN'T RUN THIS TEST. ** //
     test("Connectomics + tracking + infant profiles - should run successfully") {
 
         when {
@@ -98,10 +122,9 @@ nextflow_pipeline {
 
         then {
             assert workflow.success
-            assert workflow.trace.tasks().size() == 35
+            assert workflow.trace.tasks().size() == 34
         }
 
     }
-*/
 
 }
diff --git a/tests/tracking.nf.test b/tests/tracking.nf.test
@@ -20,7 +20,7 @@ nextflow_pipeline {
 
         then {
             assert workflow.success
-            assert workflow.trace.tasks().size() == 26
+            assert workflow.trace.tasks().size() == 25
         }
 
     }
@@ -92,7 +92,7 @@ nextflow_pipeline {
 
         then {
             assert workflow.success
-            assert workflow.trace.tasks().size() == 29
+            assert workflow.trace.tasks().size() == 28
         }
 
     }

diff --git a/workflows/pediatric.nf b/workflows/pediatric.nf
@@ -160,8 +160,8 @@ workflow PEDIATRIC {
 
         PREPROC_DWI(
             ch_inputs.dwi_bval_bvec,
-            [],
-            [],
+            Channel.empty(),
+            Channel.empty(),
             ch_inputs.rev_b0,
             ch_topup_config,
             ch_dwi_weights