[FIX] infant profile issues + better assertions for failed test + tes…

…t cases

conf/modules.config

@@ -88,6 +88,20 @@ process {
 
     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' {
@@ -182,6 +196,25 @@ process {
         ext.ventricles_mask = true
     }
 
+    withName: 'NF_PEDIATRIC:PEDIATRIC:RESAMPLE_T2' {
+        ext.voxel_size = params.t1_resample_voxel_size
+        ext.interp = params.t1_resample_interp
+    }
+
+    withName: 'NF_PEDIATRIC:PEDIATRIC:RESAMPLE_WMMASK' {
+        ext.voxel_size = params.t1_resample_voxel_size
+        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:MASK_COMBINE' {
         ext.local_fa_seeding_mask_thr = params.local_fa_seeding_mask_threshold
     }
@@ -190,6 +223,7 @@ process {
         ext.dimensionality = params.reg_dimensionality
         ext.interpolation = params.reg_interpolation
         ext.output_dtype = params.reg_output_dtype
+        ext.first_suffix = "wm_mask"
     }
 
     withName: 'NF_PEDIATRIC:PEDIATRIC:TRACKING_PFTTRACKING' {

modules/local/connectivity/metrics.nf

@@ -19,46 +19,83 @@ process CONNECTIVITY_METRICS {
     script:
     def prefix = task.ext.prefix ?: "${meta.id}"
 
-    String metrics_list = metrics.join(", ").replace(',', '')
-
-    """
-    metrics_args=""
-
-    for metric in $metrics_list; do
-        base_name=\$(basename \${metric})
-        metrics_args="\${metrics_args} --metrics \${metric} \$(basename \$base_name .nii.gz).npy"
-    done
-
-    scil_connectivity_compute_matrices.py $h5 $labels \
-        --processes $task.cpus \
-        --volume "${prefix}__vol.npy" \
-        --streamline_count "${prefix}__sc.npy" \
-        --length "${prefix}__len.npy" \
-        \$metrics_args \
-        --density_weighting \
-        --no_self_connection \
-        --include_dps ./ \
-        --force_labels_list $labels_list
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
-    END_VERSIONS
-    """
+    if ( metrics ) {
+        metrics_list = metrics.join(", ").replace(',', '')
+
+        """
+        metrics_args=""
+
+        for metric in $metrics_list; do
+            base_name=\$(basename \${metric})
+            metrics_args="\${metrics_args} --metrics \${metric} \$(basename \$base_name .nii.gz).npy"
+        done
+
+        scil_connectivity_compute_matrices.py $h5 $labels \
+            --processes $task.cpus \
+            --volume "${prefix}__vol.npy" \
+            --streamline_count "${prefix}__sc.npy" \
+            --length "${prefix}__len.npy" \
+            \$metrics_args \
+            --density_weighting \
+            --no_self_connection \
+            --include_dps ./ \
+            --force_labels_list $labels_list
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
+        END_VERSIONS
+        """
+    } else {
+        """
+        scil_connectivity_compute_matrices.py $h5 $labels \
+            --processes $task.cpus \
+            --volume "${prefix}__vol.npy" \
+            --streamline_count "${prefix}__sc.npy" \
+            --length "${prefix}__len.npy" \
+            --density_weighting \
+            --no_self_connection \
+            --include_dps ./ \
+            --force_labels_list $labels_list
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
+        END_VERSIONS
+        """
+    }
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
 
-    """
-    touch ${prefix}__vol.npy
-    touch ${prefix}__sc.npy
-    touch ${prefix}__len.npy
+    if ( metrics ) {
+        metrics_list = metrics.join(", ").replace(',', '')
+
+        """
+        for metric in $metrics_list; do
+            base_name=\$(basename "\${metric}" .nii.gz)
+            touch "\${base_name}.npy"
+        done
+
+        scil_connectivity_compute_matrices.py -h
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
+        END_VERSIONS
+        """
+    } else {
+        """
+        touch ${prefix}__vol.npy
+        touch ${prefix}__sc.npy
+        touch ${prefix}__len.npy
 
-    scil_connectivity_compute_matrices.py -h
+        scil_connectivity_compute_matrices.py -h
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
-    END_VERSIONS
-    """
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
+        END_VERSIONS
+        """
+    }
 }

modules/local/image/convert.nf

@@ -0,0 +1,49 @@
+process IMAGE_CONVERT {
+    tag "$meta.id"
+    label 'process_single'
+
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://scil.usherbrooke.ca/containers/scilus_2.0.2.sif':
+        'scilus/scilus:2.0.2' }"
+
+    input:
+    tuple val(meta), path(image)
+
+    output:
+    tuple val(meta), path("*_converted.nii.gz")     , emit: image
+    path "versions.yml"                             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    def datatype = task.ext.datatype ? "--data_type ${task.ext.datatype}" : "--data_type uint8"
+    def suffix = task.ext.first_suffix ? "${task.ext.first_suffix}_${task.ext.datatype}_converted" : "${task.ext.datatype}_converted"
+
+    """
+    scil_volume_math.py convert $image ${prefix}_${suffix}.nii.gz $datatype
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    def suffix = task.ext.first_suffix ? "${task.ext.first_suffix}_${task.ext.datatype}" : "${task.ext.datatype}"
+
+    """
+    touch ${prefix}_${suffix}.nii.gz
+
+    scil_volume_math.py -h
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
+    END_VERSIONS
+    """
+}

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

@@ -2,7 +2,7 @@ process BETCROP_SYNTHBET {
     tag "$meta.id"
     label 'process_single'
 
-    container "freesurfer/synthstrip:latest"
+    container "freesurfer/freesurfer:7.4.1"
     containerOptions "--entrypoint ''"
 
     input:

subworkflows/local/utils_nfcore_pediatric_pipeline/main.nf

@@ -133,7 +133,7 @@ workflow PIPELINE_INITIALISATION {
                         error("Please provide a warp image for sample: ${meta.id}")
                     }
                     if (!metrics) {
-                        error("You did not provide metric file for sample: ${meta.id}")
+                        log.warn("You did not provide metric file for sample: ${meta.id}")
                     }
                 }
 
@@ -214,12 +214,12 @@ workflow PIPELINE_INITIALISATION {
                         error("Please provide a warp image for sample: ${meta.id}")
                     }
                     if (!metrics) {
-                        error("You did not provide metric file for sample: ${meta.id}")
+                        log.warn("You did not provide metric file for sample: ${meta.id}")
                     }
                 }
 
                 // ** Validate files for profile children with tracking and connectomics. ** //
-                if ( params.tracking && params.connectomics && !params.infant ) {
+                if ( params.tracking && params.connectomics && !params.infant && !params.freesurfer ) {
                     if (!t1) {
                         error("Please provide a T1w image for sample: ${meta.id}")
                     }
@@ -270,7 +270,7 @@ workflow PIPELINE_INITIALISATION {
                         error("Please provide a warp image for sample: ${meta.id}")
                     }
                     if (!metrics) {
-                        error("You did not provide metric file for sample: ${meta.id}")
+                        log.warn("You did not provide metric file for sample: ${meta.id}")
                     }
                 }
 

subworkflows/nf-neuro/preproc_dwi/main.nf

@@ -4,6 +4,8 @@ include { IMAGE_POWDERAVERAGE } from '../../../modules/nf-neuro/image/powderaver
 include { IMAGE_APPLYMASK as BET_DWI } from '../../../modules/nf-neuro/image/applymask/main'
 include { BETCROP_SYNTHBET } from '../../../modules/nf-neuro/betcrop/synthbet/main'
 include { BETCROP_CROPVOLUME as CROPDWI } from '../../../modules/nf-neuro/betcrop/cropvolume/main'
+include { BETCROP_CROPVOLUME as CROPMASK } from '../../../modules/nf-neuro/betcrop/cropvolume/main'
+include { IMAGE_CONVERT as CONVERT } from '../../../modules/local/image/convert'
 include { BETCROP_FSLBETCROP } from '../../../modules/nf-neuro/betcrop/fslbetcrop/main'
 include { BETCROP_CROPVOLUME as CROPB0 } from '../../../modules/nf-neuro/betcrop/cropvolume/main'
 include { PREPROC_N4 as N4_DWI } from '../../../modules/nf-neuro/preproc/n4/main'
@@ -106,8 +108,16 @@ workflow PREPROC_DWI {
                 .map{ it + [[]] })
             ch_versions = ch_versions.mix(CROPDWI.out.versions.first())
 
+            ch_cropmask = BETCROP_SYNTHBET.out.brain_mask
+                .join(CROPDWI.out.bounding_box)
+            CROPMASK ( ch_cropmask )
+            ch_versions = ch_versions.mix(CROPMASK.out.versions.first())
+
+            CONVERT ( CROPMASK.out.image )
+            ch_versions = ch_versions.mix(CONVERT.out.versions.first())
+
             ch_dwi = CROPDWI.out.image
-            ch_mask = BETCROP_SYNTHBET.out.brain_mask
+            ch_mask = CONVERT.out.image
             ch_bbox = CROPDWI.out.bounding_box
 
         } else {

tests/data/samplesheet_testall_infant.csv

@@ -0,0 +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-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/rev_b0.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/labels.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/wm_mask.nii.gz,,,,,,,

tests/data/samplesheet_testconn_infant.csv

@@ -0,0 +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/,

tests/data/samplesheet_testconn_notrk.csv

@@ -0,0 +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/,

tests/data/samplesheet_testtracking_withmetrics.csv

@@ -0,0 +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-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/rev_b0.nii.gz,,,,,,,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/metrics,