move checkup to workflow, update docs, and tests

scilus · Jan 9, 2025 · 8b8e8ab · 8b8e8ab
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased] - [2025-01-08]
 
+### `Added`
+
+- Required --dti_shells and --fodf_shells parameters.
+
 ### `Changed`
 
 - Fastsurfer and freesurfer outputs are now in their own dedicated output folder.

diff --git a/docs/usage.md b/docs/usage.md
@@ -122,10 +122,10 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p
 The typical command for running the pipeline is as follows:
 
 ```bash
-nextflow run scilus/nf-pediatric -r main --input ./samplesheet.csv --outdir ./results -profile docker
+nextflow run scilus/nf-pediatric -r main --input ./samplesheet.csv --outdir ./results --dti_shells "0 1000" --fodf_shells "0 1000" -profile docker
 ```
 
-This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles.
+This will launch the pipeline with the `docker` configuration profile. There is only 4 parameters that need to be supplied at runtime: `--input`: for the path to your samplesheet, `--oudir`: path to the output directory, `--dti_shells`: if the tracking profile is selected, you need to identify which shell to use for DTI fitting (0 and 1000 were selected in the previous example), and `--fodf_shells`: if the tracking profile is selected, specify your shells as for the DTI parameter. See below for more information about profiles.
 
 Note that the pipeline will create the following files in your working directory:
 

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -406,7 +406,6 @@
             "fa_icon": "fas fa-brain",
             "description": "Options for DTI processing.",
             "help_text": "These options are used to configure the DTI processing steps in the pipeline. You can use these options to customise the behaviour of the DTI processing steps.",
-            "required": ["dti_shells"],
             "properties": {
                 "dti_shell_tolerance": {
                     "type": "integer",
@@ -537,7 +536,6 @@
             "fa_icon": "fas fa-brain",
             "description": "Options for FODF processing.",
             "help_text": "These options are used to configure the FODF processing steps in the pipeline. You can use these options to customise the behaviour of the FODF processing steps.",
-            "required": ["fodf_shells"],
             "properties": {
                 "fodf_shell_tolerance": {
                     "type": "integer",

diff --git a/tests/chained.nf.test b/tests/chained.nf.test
@@ -53,6 +53,9 @@ nextflow_pipeline {
                 params.connectomics = true
                 params.tracking = true
 
+                params.dti_shells = "0 1000"
+                params.fodf_shells = "0 1000"
+
             }
         }
 
@@ -85,6 +88,9 @@ nextflow_pipeline {
                 params.tracking = true
                 params.freesurfer = true
 
+                params.dti_shells = "0 1000"
+                params.fodf_shells = "0 1000"
+
                 params.use_fastsurfer = true
                 params.fs_license = "https://www.dropbox.com/scl/fi/0s8lp6lydyd0rxawxb4jm/license.txt?rlkey=hz54oc0d4sor69avqphtrjvgn&st=9e0yij97&dl=0"
             }
@@ -122,6 +128,9 @@ nextflow_pipeline {
                 params.connectomics = true
                 params.tracking = true
 
+                params.dti_shells = "0 1000"
+                params.fodf_shells = "0 1000"
+
             }
         }
 
@@ -164,6 +173,9 @@ nextflow_pipeline {
                 params.local_min_len                    = 15
                 params.local_fa_seeding_mask_threshold  = 0.10
 
+                params.dti_shells = "0 1000"
+                params.fodf_shells = "0 1000"
+
             }
         }
 

diff --git a/tests/multisubjects.nf.test b/tests/multisubjects.nf.test
@@ -14,6 +14,9 @@ nextflow_pipeline {
                 params.outdir = "$outputDir"
                 params.use_fastsurfer = true
 
+                params.dti_shells = "0 1000"
+                params.fodf_shells = "0 1000"
+
                 params.connectomics = true
                 params.tracking = true
                 params.freesurfer = true
@@ -55,6 +58,9 @@ nextflow_pipeline {
                 params.tracking = true
                 params.infant = true
 
+                params.dti_shells = "0 1000"
+                params.fodf_shells = "0 1000"
+
                 // ** Infant specific parameters ** //
                 params.dwi_run_synthstrip               = true
                 params.dwi_normalize_fa_mask_threshold  = 0.10

diff --git a/tests/tracking.nf.test b/tests/tracking.nf.test
@@ -13,6 +13,9 @@ nextflow_pipeline {
                 params.input = "$projectDir/tests/data/samplesheet_testtracking.csv"
                 params.outdir = "$outputDir"
 
+                params.dti_shells = "0 1000"
+                params.fodf_shells = "0 1000"
+
                 params.tracking = true
 
             }
@@ -43,6 +46,9 @@ nextflow_pipeline {
                 params.input = "$projectDir/tests/data/samplesheet_testtracking.csv"
                 params.outdir = "$outputDir"
 
+                params.dti_shells = "0 1000"
+                params.fodf_shells = "0 1000"
+
                 params.tracking = true
                 params.skip_dwi_preprocessing = true
 
@@ -76,6 +82,9 @@ nextflow_pipeline {
 
                 params.tracking = true
 
+                params.dti_shells = "0 1000"
+                params.fodf_shells = "0 1000"
+
             }
         }
 
@@ -85,6 +94,48 @@ nextflow_pipeline {
         }
     }
 
+    test("Tracking profile no dti shells - should fail") {
+
+        when {
+            params {
+
+                params.input = "$projectDir/tests/data/samplesheet_testtracking_norev.csv"
+                params.outdir = "$outputDir"
+
+                params.tracking = true
+
+                params.fodf_shells = "0 1000"
+
+            }
+        }
+
+        then {
+            assert workflow.failed
+            assert workflow.stdout.contains("Please provide the DTI shells using --dti_shells parameter")
+        }
+    }
+
+    test("Tracking profile no fodf shells - should fail") {
+
+        when {
+            params {
+
+                params.input = "$projectDir/tests/data/samplesheet_testtracking_norev.csv"
+                params.outdir = "$outputDir"
+
+                params.tracking = true
+
+                params.dti_shells = "0 1000"
+
+            }
+        }
+
+        then {
+            assert workflow.failed
+            assert workflow.stdout.contains("Please provide the FODF shells using --fodf_shells parameter")
+        }
+    }
+
     test("Tracking profile no dwi - should fail") {
 
         when {
@@ -93,6 +144,9 @@ nextflow_pipeline {
                 params.input = "$projectDir/tests/data/samplesheet_testtracking_nodwi.csv"
                 params.outdir = "$outputDir"
 
+                params.dti_shells = "0 1000"
+                params.fodf_shells = "0 1000"
+
                 params.tracking = true
 
             }
@@ -126,6 +180,9 @@ nextflow_pipeline {
                 params.local_fa_seeding_mask_threshold  = 0.10
                 params.run_local_tracking               = true
 
+                params.dti_shells = "0 1000"
+                params.fodf_shells = "0 1000"
+
             }
         }
 
@@ -167,6 +224,9 @@ nextflow_pipeline {
                 params.local_min_len                    = 15
                 params.local_fa_seeding_mask_threshold  = 0.10
 
+                params.dti_shells = "0 1000"
+                params.fodf_shells = "0 1000"
+
             }
         }
 
@@ -187,6 +247,9 @@ nextflow_pipeline {
                 params.tracking = true
                 params.infant = true
 
+                params.dti_shells = "0 1000"
+                params.fodf_shells = "0 1000"
+
                 // ** Infant specific parameters ** //
                 params.dwi_run_synthstrip               = true
                 params.dwi_normalize_fa_mask_threshold  = 0.10
@@ -217,6 +280,9 @@ nextflow_pipeline {
                 params.tracking = true
                 params.infant = true
 
+                params.dti_shells = "0 1000"
+                params.fodf_shells = "0 1000"
+
                 // ** Infant specific parameters ** //
                 params.dwi_run_synthstrip               = true
                 params.dwi_normalize_fa_mask_threshold  = 0.10

diff --git a/workflows/pediatric.nf b/workflows/pediatric.nf
@@ -152,6 +152,9 @@ workflow PEDIATRIC {
     //
     if ( params.tracking ) {
 
+        if ( !params.dti_shells ) { error "Please provide the DTI shells using --dti_shells parameter" }
+        if ( !params.fodf_shells ) { error "Please provide the FODF shells using --fodf_shells parameter" }
+
         /* Load topup config if provided */
         if ( params.dwi_susceptibility_config_file ) {
             if ( file(params.dwi_susceptibility_config_file).exists() ) {