Add eddy qc

assets/multiqc_config.yml

@@ -3,18 +3,23 @@ report_comment: >
   analysis pipeline.
 
 report_section_order:
-  pre_qc_rgb:
+  framewise_displacement:
     order: -200
-  pre_qc_sampling_mqc:
+  pre_qc_rgb:
     order: -300
-  registration_qc:
+  pre_qc_sampling_mqc:
     order: -500
-  dti_qc:
+  registration_qc:
     order: -600
+  dti_qc:
+    order: -700
   tracking_mask_qc:
-    order: -700    
+    order: -800    
   tracking_qc:
-    order: -800
+    order: -900
+
+module_order:
+  - framewise_displacement
 
 custom_data:
   pre_qc_rgb:
@@ -78,6 +83,8 @@ custom_data:
     plot_type: "image"
 
 sp:
+  framewise_displacement:
+    fn: "*dwi_eddy_restricted_movement_rms.txt"
   pre_qc_rgb:
     fn: "*rgb_mqc.png"
   pre_qc_sampling_mqc:
@@ -89,4 +96,12 @@ sp:
   tracking_mask_qc:
     fn: "*_mask_tracking_mqc.png"
   tracking_qc:
-    fn: "*local_tracking_mqc.png"
+    fn: "*local_tracking_mqc.png"
+
+# Customisable module parameters
+framewise_displacement:
+  warn_threshold: 0.05
+  fail_threshold: 0.12
+  unit: "µm"
+
+export_plots: true

main.nf

@@ -145,6 +145,7 @@ workflow {
         ch_after_eddy = PREPROC_SINGLEEDDY.out.dwi_corrected.join(
             PREPROC_SINGLEEDDY.out.bval_corrected).join(
             PREPROC_SINGLEEDDY.out.bvec_corrected)
+        ch_multiqc_files = ch_multiqc_files.mix(PREPROC_SINGLEEDDY.out.eddy_fd_mqc)
     }
     else {
         ch_after_eddy = ch_eddy
@@ -160,8 +161,9 @@ workflow {
     }
     else {
         ch_nnunet = ch_after_eddy.join(UTILS_EXTRACTB0.out.b0)
-                .map { meta, dwi, bval, bvec, b0 ->   
-                    [meta, dwi, bval, b0 ?: [   ]]}
+        .join(data.mask, by: 0, remainder: true)
+                .map { meta, dwi, bval, bvec, b0, mask ->   
+                    [meta, dwi, bval, b0, mask ?: [   ]]}
 
         NNUNET(ch_nnunet)
 

modules.json

@@ -7,7 +7,7 @@
         "nf-core": {
           "multiqc": {
             "branch": "master",
-            "git_sha": "e10b76ca0c66213581bec2833e30d31f239dec0b",
+            "git_sha": "98403d15b0e50edae1f3fec5eae5e24982f1fade",
             "installed_by": ["modules"]
           }
         }

modules/local/preproc/singleeddy/main.nf

@@ -7,10 +7,11 @@ process PREPROC_SINGLEEDDY {
     input:
         tuple val(meta), path(dwi), path(bval), path(bvec)
     output:
-        tuple val(meta), path("*__dwi_eddy_corrected.nii.gz")   , emit: dwi_corrected
-        tuple val(meta), path("*__dwi_eddy_corrected.bval")     , emit: bval_corrected
-        tuple val(meta), path("*__dwi_eddy_corrected.bvec")     , emit: bvec_corrected
-        path "versions.yml"                                     , emit: versions
+        tuple val(meta), path("*__dwi_eddy_corrected.nii.gz")               , emit: dwi_corrected
+        tuple val(meta), path("*__dwi_eddy_corrected.bval")                 , emit: bval_corrected
+        tuple val(meta), path("*__dwi_eddy_corrected.bvec")                 , emit: bvec_corrected
+        tuple val(meta), path("*__dwi_eddy_restricted_movement_rms.txt")    , emit: eddy_fd_mqc, optional:true
+        path "versions.yml"                                                 , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -42,9 +43,11 @@ process PREPROC_SINGLEEDDY {
 
     echo "--nthr=$extra_thr --very_verbose $extra_args --niter=$extra_ite" >> eddy.sh
 	sh eddy.sh
-	mv ${prefix}__.nii.gz ${prefix}__dwi_eddy_corrected.nii.gz
+    mv ${prefix}__.nii.gz ${prefix}__dwi_eddy_corrected.nii.gz
 	mv ${prefix}__.eddy_rotated_bvecs ${prefix}__dwi_eddy_corrected.bvec
     mv ${bval} ${prefix}__dwi_eddy_corrected.bval
+    mv ${prefix}__.eddy_restricted_movement_rms ${prefix}__dwi_eddy_restricted_movement_rms.txt
+
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -63,6 +66,7 @@ process PREPROC_SINGLEEDDY {
     touch ${prefix}__dwi_eddy_corrected.nii.gz
     touch ${prefix}__dwi_eddy_corrected.bval
     touch ${prefix}__dwi_eddy_corrected.bvec
+    touch ${prefix}__dwi_eddy_restricted_movement_rms.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/local/preproc/singleeddy/meta.yml

@@ -62,6 +62,15 @@ output:
       description: B-vectors corrected in FSL format
       pattern: "*__dwi_eddy_corrected.bvec"
 
+  - eddy_fd_mqc:
+      - "*__dwi_eddy_restricted_movement_rms.txt":
+          type: file
+          description: |
+            Text file containing framewise displacement (restricted movement)
+            information from eddy. Made for use in MultiQC report.
+          pattern: "*__dwi_eddy_restricted_movement_rms.txt"
+          ontologies: []
+
   - versions:
       type: file
       description: File containing software versions