Merge pull request #53 from ThoumyreStanislas/fix-container-synthbet

change version container synthbet (Answer issue 41)
scilus · Nov 25, 2024 · 904b438 · 904b438
2 parents 6a2f58e + fe126ac
commit 904b438
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Showing 5 changed files with 15 additions and 14 deletions.
diff --git a/.github/workflows/run_checks_suite.yml b/.github/workflows/run_checks_suite.yml
@@ -156,6 +156,8 @@ jobs:
             path: modules/nf-neuro/registration/easyreg
           - runner: scilus-nf-neuro-bigmem-runners
             path: modules/nf-neuro/segmentation/synthseg
+          - runner: scilus-nf-neuro-bigmem-runners
+            path: modules/nf-neuro/betcrop/synthbet
           - runner: scilus-nf-neuro-bigmem-runners
             path: modules/nf-neuro/registration/synthregistration
           - runner: scilus-nf-neuro-bigmem-runners

diff --git a/modules/nf-neuro/betcrop/synthbet/main.nf b/modules/nf-neuro/betcrop/synthbet/main.nf
@@ -2,8 +2,7 @@ process BETCROP_SYNTHBET {
     tag "$meta.id"
     label 'process_single'
 
-    container "freesurfer/synthstrip:latest"
-    containerOptions "--entrypoint ''"
+    container "freesurfer/freesurfer:7.4.1"
 
     input:
     tuple val(meta), path(image), path(weights) /* optional, input = [] */
@@ -33,7 +32,7 @@ process BETCROP_SYNTHBET {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        freesurfer: 7.4
+        Freesurfer: \$(mri_convert -version | grep "freesurfer" | sed -E 's/.* ([0-9]+\\.[0-9]+\\.[0-9]+).*/\\1/')
     END_VERSIONS
     """
 
@@ -48,7 +47,7 @@ process BETCROP_SYNTHBET {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        freesurfer: 7.4
+        Freesurfer: \$(mri_convert -version | grep "freesurfer" | sed -E 's/.* ([0-9]+\\.[0-9]+\\.[0-9]+).*/\\1/')
     END_VERSIONS
     """
 }
diff --git a/modules/nf-neuro/betcrop/synthbet/tests/main.nf.test.snap b/modules/nf-neuro/betcrop/synthbet/tests/main.nf.test.snap
@@ -21,7 +21,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,f0a96d8fd7ca9d9935818dceaf91f457"
+                    "versions.yml:md5,c639461870ca534b5105f61d672f740f"
                 ],
                 "bet_image": [
                     [
@@ -42,14 +42,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,f0a96d8fd7ca9d9935818dceaf91f457"
+                    "versions.yml:md5,c639461870ca534b5105f61d672f740f"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-06-11T14:52:54.970673"
+        "timestamp": "2024-11-25T18:19:01.459548926"
     }
 }
diff --git a/modules/nf-neuro/betcrop/synthbet/tests/nextflow.config b/modules/nf-neuro/betcrop/synthbet/tests/nextflow.config
@@ -1,7 +1,7 @@
 process {
     withName: "BETCROP_SYNTHBET" {
         publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-        memory = 8.GB
+        memory = 10.GB
         ext.nocsf = true
     }
 }
diff --git a/subworkflows/nf-neuro/preproc_t1/tests/main.nf.test.snap b/subworkflows/nf-neuro/preproc_t1/tests/main.nf.test.snap
@@ -18,9 +18,9 @@
             "test_cropped.nii.gz:md5:header,efab188f3700b5b29d4b4ef99cec1295,data,e551be653d402018fd73a4f708b1641e",
             "test_t1_cropped.nii.gz:md5:header,efab188f3700b5b29d4b4ef99cec1295,data,8a93b9d76ead7dae4af4792b9cf70479",
             [
+                "versions.yml:md5,318cabe934be45528a25f52083d9c90d",
                 "versions.yml:md5,37229cd5cee6f6788fbc9083d6618c61",
                 "versions.yml:md5,657fbb224f260392e573b8511c4b798d",
-                "versions.yml:md5,9d515db259af59f33ccd14061fbc45d1",
                 "versions.yml:md5,b979132991d8f72a3585465533bd5730",
                 "versions.yml:md5,bdd934b4b8456060c36d6d97e4f30740",
                 "versions.yml:md5,ea32c30f5320f720b2f5dc32ac2535ea"
@@ -30,7 +30,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-11-05T18:33:42.260959257"
+        "timestamp": "2024-11-25T18:23:03.990173398"
     },
     "preproc_t1_option": {
         "content": [
@@ -51,9 +51,9 @@
             "test_cropped.nii.gz:md5:header,efab188f3700b5b29d4b4ef99cec1295,data,3f64b48b555fd40a3dfc73e6c5ccce5e",
             "test_t1_cropped.nii.gz:md5:header,efab188f3700b5b29d4b4ef99cec1295,data,f3af6e0383ac738415c578c42969e6a9",
             [
+                "versions.yml:md5,318cabe934be45528a25f52083d9c90d",
                 "versions.yml:md5,37229cd5cee6f6788fbc9083d6618c61",
                 "versions.yml:md5,657fbb224f260392e573b8511c4b798d",
-                "versions.yml:md5,9d515db259af59f33ccd14061fbc45d1",
                 "versions.yml:md5,b979132991d8f72a3585465533bd5730",
                 "versions.yml:md5,bdd934b4b8456060c36d6d97e4f30740",
                 "versions.yml:md5,ea32c30f5320f720b2f5dc32ac2535ea"
@@ -63,7 +63,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-11-05T18:33:00.128245652"
+        "timestamp": "2024-11-25T18:22:27.118657583"
     },
     "preproc_t1_classic": {
         "content": [