Merge pull request #75 from ThoumyreStanislas/mrtrix_nlmeans

#45 MRtrix module - denoising/mppca
scilus · Dec 18, 2024 · 9bd2a96 · 9bd2a96
2 parents a7dde7f + fb5ae93
commit 9bd2a96
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Showing 4 changed files with 19 additions and 26 deletions.
diff --git a/modules/nf-neuro/denoising/mppca/main.nf b/modules/nf-neuro/denoising/mppca/main.nf
@@ -3,9 +3,7 @@ process DENOISING_MPPCA {
     tag "$meta.id"
     label 'process_medium'
 
-    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' }"
+    container "mrtrix3/mrtrix3:latest"
 
     input:
     tuple val(meta), path(dwi), path(mask)
@@ -30,13 +28,12 @@ process DENOISING_MPPCA {
     export MRTRIX_RNG_SEED=112524
 
     dwidenoise $dwi ${prefix}_dwi_denoised.nii.gz $extent ${args.join(" ")}
-    scil_volume_math.py lower_clip ${prefix}_dwi_denoised.nii.gz 0 \
-        ${prefix}_dwi_denoised.nii.gz -f
+    mrcalc ${prefix}_dwi_denoised.nii.gz 0 -gt ${prefix}_dwi_denoised.nii.gz 0 \
+        -if ${prefix}_dwi_denoised.nii.gz -force
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         mrtrix: \$(mrcalc -version 2>&1 | sed -n 's/== mrcalc \\([0-9.]\\+\\).*/\\1/p')
-        scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
     END_VERSIONS
     """
 
@@ -46,14 +43,13 @@ process DENOISING_MPPCA {
 
     """
     dwidenoise -h
-    scil_volume_math.py -h
+    mrcalc -h
 
     touch ${prefix}_dwi_denoised.nii.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         mrtrix: \$(mrcalc -version 2>&1 | sed -n 's/== mrcalc \\([0-9.]\\+\\).*/\\1/p')
-        scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
     END_VERSIONS
     """
 }
diff --git a/modules/nf-neuro/denoising/mppca/meta.yml b/modules/nf-neuro/denoising/mppca/meta.yml
@@ -12,9 +12,6 @@ tools:
   - "MRtrix3":
       description: "Toolbox for image processing, analysis and visualisation of dMRI."
       homepage: "https://mrtrix.readthedocs.io/en/latest/"
-  - "scilpy":
-      description: "The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox."
-      homepage: "https://github.com/scilus/scilpy.git"
 
 input:
   - meta:

diff --git a/modules/nf-neuro/denoising/mppca/tests/main.nf.test.snap b/modules/nf-neuro/denoising/mppca/tests/main.nf.test.snap
@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,c9915fbc1956d7f54bee0748f1ddf920"
+                    "versions.yml:md5,adbce7b09c63d541cdc2782235363275"
                 ],
                 "image": [
                     [
@@ -22,14 +22,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,c9915fbc1956d7f54bee0748f1ddf920"
+                    "versions.yml:md5,adbce7b09c63d541cdc2782235363275"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0-rc1",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-08-05T15:17:51.718413"
+        "timestamp": "2024-12-12T18:27:14.057961679"
     }
 }
diff --git a/subworkflows/nf-neuro/preproc_dwi/tests/main.nf.test.snap b/subworkflows/nf-neuro/preproc_dwi/tests/main.nf.test.snap
@@ -15,10 +15,10 @@
                 "versions.yml:md5,0494fbf74bc9c16d2b30cb45b3bba66b",
                 "versions.yml:md5,0b8c908e52917b0b706fc9d1b4d6cd24",
                 "versions.yml:md5,0e680a0c6b56892e1a7ec7f85bb95322",
-                "versions.yml:md5,3340c4b5e56ca52f7342be3c9044eb47",
+                "versions.yml:md5,571265e710ca29198e69be22c0f970d5",
+                "versions.yml:md5,662ea558da42564a0f6140473132bcb4",
                 "versions.yml:md5,7ddf2e98f59b19c9b933670550f26ad7",
                 "versions.yml:md5,c15ba5efd24564dba4710b6da8c4b791",
-                "versions.yml:md5,d68fe3399120f84f1add62181708780b",
                 "versions.yml:md5,ea5858879452a59bb355228ae7f38111",
                 "versions.yml:md5,f041502e22449973d84ac1c618e8ebf9"
             ],
@@ -32,9 +32,9 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-01T12:50:45.411022164"
+        "timestamp": "2024-12-12T18:30:03.433004717"
     },
     "preproc_dwi_rev_b0": {
         "content": [
@@ -52,7 +52,7 @@
                 "versions.yml:md5,0494fbf74bc9c16d2b30cb45b3bba66b",
                 "versions.yml:md5,0b8c908e52917b0b706fc9d1b4d6cd24",
                 "versions.yml:md5,0e680a0c6b56892e1a7ec7f85bb95322",
-                "versions.yml:md5,3340c4b5e56ca52f7342be3c9044eb47",
+                "versions.yml:md5,571265e710ca29198e69be22c0f970d5",
                 "versions.yml:md5,7ddf2e98f59b19c9b933670550f26ad7",
                 "versions.yml:md5,c15ba5efd24564dba4710b6da8c4b791",
                 "versions.yml:md5,ea5858879452a59bb355228ae7f38111",
@@ -68,9 +68,9 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-01T12:49:12.328235961"
+        "timestamp": "2024-12-12T18:28:35.975149345"
     },
     "preproc_dwi_all_options": {
         "content": [
@@ -88,10 +88,10 @@
                 "versions.yml:md5,0494fbf74bc9c16d2b30cb45b3bba66b",
                 "versions.yml:md5,0b8c908e52917b0b706fc9d1b4d6cd24",
                 "versions.yml:md5,0e680a0c6b56892e1a7ec7f85bb95322",
-                "versions.yml:md5,3340c4b5e56ca52f7342be3c9044eb47",
+                "versions.yml:md5,571265e710ca29198e69be22c0f970d5",
+                "versions.yml:md5,662ea558da42564a0f6140473132bcb4",
                 "versions.yml:md5,7ddf2e98f59b19c9b933670550f26ad7",
                 "versions.yml:md5,c15ba5efd24564dba4710b6da8c4b791",
-                "versions.yml:md5,d68fe3399120f84f1add62181708780b",
                 "versions.yml:md5,ea5858879452a59bb355228ae7f38111",
                 "versions.yml:md5,f041502e22449973d84ac1c618e8ebf9"
             ],
@@ -107,6 +107,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-29T13:47:57.561745796"
+        "timestamp": "2024-12-12T18:31:26.492075412"
     }
 }