use gpu+docker/singularity profile for nf-test

.github/workflows/nf-test-gpu.yml

@@ -68,7 +68,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        profile: [singularity_gpu, docker_gpu]
+        profile: [docker, singularity]
         shard: ${{ fromJson(needs.get-shards.outputs.shard) }}
         NXF_VER:
           - "24.10.2"
@@ -83,7 +83,7 @@ jobs:
       - name: Run nf-test Action
         uses: ./.github/actions/nf-test
         with:
-          profile: ${{ matrix.profile }},gpu
+          profile: ${{ matrix.profile }}+gpu
           shard: ${{ matrix.shard }}
           total_shards: ${{ needs.get-shards.outputs.total_shards }}
           filters: ${{ matrix.filters }}

tests/nextflow.config

@@ -26,21 +26,6 @@ process {
     ]
 }
 
-profiles {
-    singularity_gpu {
-        singularity.enabled     = true
-        singularity.autoMounts  = true
-        singularity.runOptions  = '--nv'
-        use_gpu                 = true
-    }
-    docker_gpu {
-        docker.enabled      = true
-        docker.fixOwnership = true
-        docker.runOptions   = '-u $(id -u):$(id -g) --gpus all'
-        use_gpu             = true
-    }
-}
-
 // Impose same minimum Nextflow version as the pipeline for testing
 manifest {
     nextflowVersion = '!>=24.10.2'