Use docker,singularity profile names instead of seqera_containers prefix

seqeralabs · Jun 19, 2024 · e83c4c7 · e83c4c7
1 parent 7fa7048
commit e83c4c7
Showing 1 changed file with 24 additions and 4 deletions.
diff --git a/nextflow.config b/nextflow.config
@@ -69,10 +69,6 @@ profiles {
         wave.freeze             = true
         wave.strategy           = ['conda']
     }
-    seqera_containers_docker          { includeConfig 'config/containers_docker_x86.config'        }
-    seqera_containers_docker_arm      { includeConfig 'config/containers_docker_arm64.config'      }
-    seqera_containers_singularity     { includeConfig 'config/containers_singularity_x86.config'   }
-    seqera_containers_singularity_arm { includeConfig 'config/containers_singularity_arm64.config' }
     conda {
         conda.enabled           = true
         docker.enabled          = false
@@ -94,6 +90,18 @@ profiles {
         apptainer.enabled       = false
     }
     docker {
+        includeConfig 'config/containers_docker_x86.config'
+        docker.enabled          = true
+        conda.enabled           = false
+        singularity.enabled     = false
+        podman.enabled          = false
+        shifter.enabled         = false
+        charliecloud.enabled    = false
+        apptainer.enabled       = false
+        docker.runOptions       = '-u $(id -u):$(id -g)'
+    }
+    docker_arm {
+        includeConfig 'config/containers_docker_arm64.config'
         docker.enabled          = true
         conda.enabled           = false
         singularity.enabled     = false
@@ -107,6 +115,18 @@ profiles {
         process.arch            = 'linux/arm64'
     }
     singularity {
+        includeConfig 'config/containers_singularity_x86.config'
+        singularity.enabled     = true
+        singularity.autoMounts  = true
+        conda.enabled           = false
+        docker.enabled          = false
+        podman.enabled          = false
+        shifter.enabled         = false
+        charliecloud.enabled    = false
+        apptainer.enabled       = false
+    }
+    singularity_arm {
+        includeConfig 'config/containers_singularity_arm64.config'
         singularity.enabled     = true
         singularity.autoMounts  = true
         conda.enabled           = false