[FIX] fix small issues with chaining + added assertions in test cases

.github/workflows/ci.yml

@@ -71,6 +71,8 @@ jobs:
 
       - name: Clean up Disk space
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+        with:
+          tool-cache: false
 
       - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
         run: |

modules/local/filtering/commit.nf

@@ -43,7 +43,7 @@ process FILTERING_COMMIT {
     elif [ -f "${prefix}__results_bzs/commit_1/decompose_commit.h5" ]; then
         mv "${prefix}__results_bzs/commit_1/decompose_commit.h5" "./${prefix}__decompose_commit.h5"
     else
-        mv "${prefix}__results_bzs/commit_1/essential.trk" "./${prefix}__commit.trk"
+        mv "${prefix}__results_bzs/commit_1/essential_tractogram.trk" "./${prefix}__commit.trk"
     fi
 
     cat <<-END_VERSIONS > versions.yml

modules/local/image/convert.nf

@@ -34,7 +34,7 @@ process IMAGE_CONVERT {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
 
-    def suffix = task.ext.first_suffix ? "${task.ext.first_suffix}_${task.ext.datatype}" : "${task.ext.datatype}"
+    def suffix = task.ext.first_suffix ? "${task.ext.first_suffix}_${task.ext.datatype}_converted" : "${task.ext.datatype}_converted"
 
     """
     touch ${prefix}_${suffix}.nii.gz

modules/nf-neuro/betcrop/cropvolume/main.nf

@@ -42,6 +42,7 @@ process BETCROP_CROPVOLUME {
     scil_volume_crop.py -h
 
     touch ${prefix}_${suffix}.nii.gz
+    touch bounding_box.pkl
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

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

@@ -3,8 +3,8 @@ process SEGMENTATION_FREESURFERSEG {
     label 'process_single'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://scil.usherbrooke.ca/containers/scilus_2.0.0.sif':
-        'scilus/scilus:2.0.0' }"
+        'https://scil.usherbrooke.ca/containers/scilus_2.0.2.sif':
+        'scilus/scilus:2.0.2' }"
 
     input:
         tuple val(meta), path(aparc_aseg), path(wmparc), path(lesion)
@@ -87,7 +87,7 @@ process SEGMENTATION_FREESURFERSEG {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        scilpy: 2.0.0
+        scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
         mrtrix: \$(mrconvert -version 2>&1 | sed -n 's/== mrconvert \\([0-9.]\\+\\).*/\\1/p')
     END_VERSIONS
     """
@@ -105,7 +105,7 @@ process SEGMENTATION_FREESURFERSEG {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        scilpy: 2.0.0
+        scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
         mrtrix: \$(mrconvert -version 2>&1 | sed -n 's/== mrconvert \\([0-9.]\\+\\).*/\\1/p')
     END_VERSIONS
     """

modules/nf-neuro/utils/extractb0/main.nf

@@ -3,8 +3,8 @@ process UTILS_EXTRACTB0 {
     label 'process_single'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://scil.usherbrooke.ca/containers/scilus_2.0.1.sif':
-        'scilus/scilus:2.0.1' }"
+        'https://scil.usherbrooke.ca/containers/scilus_2.0.2.sif':
+        'scilus/scilus:2.0.2' }"
 
     input:
     tuple val(meta), path(dwi), path(bval), path(bvec)
@@ -31,7 +31,7 @@ process UTILS_EXTRACTB0 {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        scilpy: 2.0.1
+        scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
     END_VERSIONS
     """
 
@@ -46,7 +46,7 @@ process UTILS_EXTRACTB0 {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        scilpy: 2.0.1
+        scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
     END_VERSIONS
     """
 }

nextflow.config

@@ -367,6 +367,15 @@ profiles {
         params.run_pft_tracking                 = false
         params.local_min_len                    = 15
         params.local_fa_seeding_mask_threshold  = 0.10
+
+        params.run_commit2                      = false
+        params.commit_para_diff                 = "1.2E-3"
+        params.commit_iso_diff                  = "2.0E-3"
+        params.commit_ball_stick                = true
+
+        params.decompose_min_len                = 10
+        params.decompose_outlier_threshold      = 0.4
+
     }
     tracking {
         params.tracking         = true

nextflow_schema.json

@@ -950,19 +950,19 @@
                     "hidden": true
                 },
                 "commit_para_diff": {
-                    "type": "number",
+                    "type": "string",
                     "description": "Para diff value used in the COMMIT filtering step.",
                     "fa_icon": "fas fa-code-branch",
                     "hidden": false
                 },
                 "commit_iso_diff": {
-                    "type": "number",
+                    "type": "string",
                     "description": "Iso diff value used in the COMMIT filtering step.",
                     "fa_icon": "fas fa-code-branch",
                     "hidden": false
                 },
                 "commit_perp_diff": {
-                    "type": "number",
+                    "type": "string",
                     "description": "Perp diff value used in the COMMIT filtering step.",
                     "fa_icon": "fas fa-code-branch",
                     "hidden": false

nf-test.config

@@ -4,7 +4,7 @@ config {
     configFile "tests/nextflow.config"
     libDir "tests/lib"
     profile "docker"
-    withTrace false
+    withTrace true
     autoSort false
     ignore "modules/**", "subworkflows/**"
     options "-dump-channels -stub-run"

tests/data/samplesheet_testconn.csv

@@ -1,2 +1,2 @@
 subject,t1,t2,dwi,bval,bvec,rev_b0,labels,wmparc,trk,peaks,fodf,mat,warp,metrics
-sub-test,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/t1.nii.gz,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/dwi.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/dwi.bval,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/dwi.bvec,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/labels.nii.gz,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/tracking.trk,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/peaks.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/fodf.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/0GenericAffine.mat,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/output1Warp.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/metrics/,
+sub-test,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/t1.nii.gz,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bval,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bvec,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/labels.nii.gz,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/tracking.trk,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/peaks.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/fodf.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/0GenericAffine.mat,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/output1Warp.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/metrics/,

tests/data/samplesheet_testconn_infant.csv

@@ -1,2 +1,2 @@
 subject,t1,t2,dwi,bval,bvec,rev_b0,labels,wmparc,trk,peaks,fodf,mat,warp,metrics
-sub-test,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/t2.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/dwi.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/dwi.bval,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/dwi.bvec,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/labels.nii.gz,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/tracking.trk,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/peaks.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/fodf.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/0GenericAffine.mat,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/output1Warp.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/metrics/,
+sub-test,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/t2.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bval,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bvec,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/labels.nii.gz,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/tracking.trk,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/peaks.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/fodf.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/0GenericAffine.mat,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/output1Warp.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/metrics/,

tests/data/samplesheet_testconn_notrk.csv

@@ -1,2 +1,2 @@
 subject,t1,t2,dwi,bval,bvec,rev_b0,labels,wmparc,trk,peaks,fodf,mat,warp,metrics
-sub-test,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/t1.nii.gz,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/dwi.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/dwi.bval,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/dwi.bvec,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/labels.nii.gz,,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/peaks.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/fodf.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/0GenericAffine.mat,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/output1Warp.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/metrics/,
+sub-test,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/t1.nii.gz,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bval,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bvec,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/labels.nii.gz,,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/peaks.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/fodf.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/0GenericAffine.mat,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/output1Warp.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/metrics/,

tests/main.nf.test

@@ -20,6 +20,7 @@ nextflow_pipeline {
 
         then {
             assert workflow.success
+            assert workflow.trace.tasks().size() == 26
         }
 
     }
@@ -84,12 +85,14 @@ nextflow_pipeline {
                 params.run_pft_tracking                 = false
                 params.local_min_len                    = 15
                 params.local_fa_seeding_mask_threshold  = 0.10
+                params.run_local_tracking               = true
 
             }
         }
 
         then {
             assert workflow.success
+            assert workflow.trace.tasks().size() == 29
         }
 
     }
@@ -105,6 +108,16 @@ nextflow_pipeline {
                 params.tracking = true
                 params.infant = true
 
+                // ** Infant specific parameters ** //
+                params.dwi_run_synthstrip               = true
+                params.dwi_normalize_fa_mask_threshold  = 0.10
+                params.fodf_max_fa_threshold            = 0.01
+                params.fodf_min_md_threshold            = 0.00185
+                params.frf_manual_frf                   = "12,5,5"
+                params.run_pft_tracking                 = false
+                params.local_min_len                    = 15
+                params.local_fa_seeding_mask_threshold  = 0.10
+
             }
         }
 
@@ -126,6 +139,16 @@ nextflow_pipeline {
                 params.tracking = true
                 params.infant = true
 
+                // ** Infant specific parameters ** //
+                params.dwi_run_synthstrip               = true
+                params.dwi_normalize_fa_mask_threshold  = 0.10
+                params.fodf_max_fa_threshold            = 0.01
+                params.fodf_min_md_threshold            = 0.00185
+                params.frf_manual_frf                   = "12,5,5"
+                params.run_pft_tracking                 = false
+                params.local_min_len                    = 15
+                params.local_fa_seeding_mask_threshold  = 0.10
+
             }
         }
 
@@ -147,6 +170,16 @@ nextflow_pipeline {
                 params.tracking = true
                 params.infant = true
 
+                // ** Infant specific parameters ** //
+                params.dwi_run_synthstrip               = true
+                params.dwi_normalize_fa_mask_threshold  = 0.10
+                params.fodf_max_fa_threshold            = 0.01
+                params.fodf_min_md_threshold            = 0.00185
+                params.frf_manual_frf                   = "12,5,5"
+                params.run_pft_tracking                 = false
+                params.local_min_len                    = 15
+                params.local_fa_seeding_mask_threshold  = 0.10
+
             }
         }
 
@@ -172,6 +205,7 @@ nextflow_pipeline {
 
         then {
             assert workflow.success
+            assert workflow.trace.tasks().size() == 7
         }
 
     }
@@ -191,6 +225,7 @@ nextflow_pipeline {
 
         then {
             assert workflow.success
+            assert workflow.trace.tasks().size() == 7
         }
 
     }
@@ -209,7 +244,7 @@ nextflow_pipeline {
         }
 
         then {
-            assert workflow.success
+            assert workflow.failed
             assert workflow.stdout.contains("Please provide a trk file for sample: sub-test")
         }
 
@@ -231,6 +266,7 @@ nextflow_pipeline {
 
         then {
             assert workflow.success
+            assert workflow.trace.tasks().size() == 7
         }
 
     }
@@ -251,6 +287,7 @@ nextflow_pipeline {
 
         then {
             assert workflow.success
+            assert workflow.trace.tasks().size() == 3
         }
 
     }
@@ -272,6 +309,7 @@ nextflow_pipeline {
 
         then {
             assert workflow.success
+            assert workflow.trace.tasks().size() == 9
         }
 
     }
@@ -294,6 +332,7 @@ nextflow_pipeline {
 
         then {
             assert workflow.success
+            assert workflow.trace.tasks().size() == 34
         }
 
     }
@@ -316,6 +355,7 @@ nextflow_pipeline {
 
         then {
             assert workflow.success
+            assert workflow.trace.tasks().size() == 34
         }
 
     }
@@ -347,6 +387,7 @@ nextflow_pipeline {
 
         then {
             assert workflow.success
+            assert workflow.trace.tasks().size() == 35
         }
 
     }

tests/nextflow.config

@@ -10,4 +10,56 @@ process {
         memory = 3.GB
         time   = 2.h
     }
+
+    withName: 'NF_PEDIATRIC:PEDIATRIC:PREPROC_T1:BETCROP_CROPVOLUME_T1' {
+        ext.output_bbox = true
+    }
+
+    withName: 'NF_PEDIATRIC:PEDIATRIC:PREPROC_DWI:CROPDWI' {
+        ext.output_bbox = true
+        ext.first_suffix = 'dwi'
+    }
+
+    withName: 'NF_PEDIATRIC:PEDIATRIC:PREPROC_DWI:CROPB0' {
+        ext.first_suffix = 'b0'
+    }
+
+    withName: 'NF_PEDIATRIC:PEDIATRIC:PREPROC_DWI:CROPMASK' {
+        ext.first_suffix = 'mask'
+    }
+
+    withName: 'NF_PEDIATRIC:PEDIATRIC:PREPROC_DWI:CONVERT' {
+        ext.first_suffix = 'mask'
+        ext.datatype = 'uint8'
+    }
+
+    withName: 'NF_PEDIATRIC:PEDIATRIC:PREPROC_DWI:BETCROP_FSLBETCROP' {
+        ext.crop = true
+    }
+
+    withName: 'NF_PEDIATRIC:PEDIATRIC:PREPROC_DWI:RESAMPLE_DWI' {
+        ext.first_suffix = 'dwi'
+    }
+
+    withName: 'NF_PEDIATRIC:PEDIATRIC:PREPROC_DWI:RESAMPLE_MASK' {
+        ext.first_suffix = 'mask'
+    }
+
+    withName: 'NF_PEDIATRIC:PEDIATRIC:RESAMPLE_WMMASK' {
+        ext.interp = "nn"
+    }
+
+    withName: 'NF_PEDIATRIC:PEDIATRIC:CROPT2' {
+        ext.output_bbox = true
+        ext.first_suffix = 't2'
+    }
+
+    withName: 'NF_PEDIATRIC:PEDIATRIC:CROPWMMASK' {
+        ext.first_suffix = 'wm_mask'
+    }
+
+    withName: 'NF_PEDIATRIC:PEDIATRIC:REGISTRATION_ANTSAPPLYTRANSFORMS' {
+        ext.first_suffix = "wm_mask"
+    }
+
 }