added gpu profile for cellpose

nf-core · Oct 30, 2024 · 5904f3e · 5904f3e
1 parent 641a0bb
commit 5904f3e
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Showing 7 changed files with 48 additions and 4 deletions.
diff --git a/.gitignore b/.gitignore
@@ -8,3 +8,4 @@ testing*
 *.pyc
 .nf-test.log
 .nf-test/
+null
diff --git a/conf/base.config b/conf/base.config
@@ -58,4 +58,7 @@ process {
     withName:'ILASTIK_PIXELCLASSIFICATION|ILASTIK_MULTICUT' {
         label = "process_high"
     }
+    withLabel:process_gpu {
+        ext.use_gpu = { use_gpu }
+    }
 }
diff --git a/modules.json b/modules.json
@@ -8,7 +8,8 @@
                     "cellpose": {
                         "branch": "master",
                         "git_sha": "7c1543a730197e2f0b8ca5141f851c4a2b08bed6",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/cellpose/cellpose.diff"
                     },
                     "deepcell/mesmer": {
                         "branch": "master",

diff --git a/modules/nf-core/cellpose/cellpose.diff b/modules/nf-core/cellpose/cellpose.diff
diff --git a/modules/nf-core/cellpose/main.nf b/modules/nf-core/cellpose/main.nf
diff --git a/nextflow.config b/nextflow.config
@@ -56,6 +56,9 @@ params {
     max_multiqc_email_size     = '25.MB'
     multiqc_methods_description = null
 
+    // GPU for segmentation
+    use_gpu                      = false
+
     // Boilerplate options
     outdir                       = null
     publish_dir_mode             = 'copy'
@@ -187,6 +190,12 @@ profiles {
     }
     test      { includeConfig 'conf/test.config'      }
     test_full { includeConfig 'conf/test_full.config' }
+    gpu {
+        docker.runOptions       = '-u $(id -u):$(id -g) --gpus device=0'
+        apptainer.runOptions    = '--no-mount tmp --writable-tmpfs --nv'
+        singularity.runOptions  = '--no-mount tmp --writable-tmpfs --nv'
+        use_gpu                 = true
+    }
 }
 
 // Load nf-core custom profiles from different Institutions

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -145,7 +145,7 @@
                 },
                 "clahe_kernel": {
                     "type": "number",
-                    "default": 25,
+                    "default": 25.0,
                     "description": "Kernel size to be used by CLAHE.",
                     "fa_icon": "far fa-object-group"
                 },
@@ -411,5 +411,10 @@
         {
             "$ref": "#/$defs/generic_options"
         }
-    ]
+    ],
+    "properties": {
+        "use_gpu": {
+            "type": "boolean"
+        }
+    }
 }
-Original file line number
+Diff line change
@@ Expand Up / @@ -8,3 +8,4 @@ testing* @@
     *.pyc
     .nf-test.log
     .nf-test/
+    null