From 96471746b9ff1bcc5e8479dd79e279002476f751 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Mon, 25 Sep 2023 18:16:50 -0500
Subject: [PATCH] feat: Replace hard-coded singularity with profile-based
 containers

---
 nextflow.config | 60 ++++++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 59 insertions(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index de600ab..4e4c25c 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -61,7 +61,65 @@ try {
     System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
 }
 
-singularity.enabled = true
+profiles {
+    docker {
+        docker.enabled = true
+        docker.userEmulation = true
+        conda.enabled = false
+        singularity.enabled = false
+        podman.enabled = false
+        shifter.enabled = false
+        charliecloud.enabled = false
+        apptainer.enabled = false
+    }
+    singularity {
+        singularity.enabled = true
+        singularity.autoMounts = true
+        conda.enabled = false
+        docker.enabled = false
+        podman.enabled = false
+        shifter.enabled = false
+        charliecloud.enabled = false
+        apptainer.enabled = false
+    }
+    podman {
+        podman.enabled = true
+        conda.enabled = false
+        docker.enabled = false
+        singularity.enabled = false
+        shifter.enabled = false
+        charliecloud.enabled = false
+        apptainer.enabled = false
+    }
+    shifter {
+        shifter.enabled = true
+        conda.enabled = false
+        docker.enabled = false
+        singularity.enabled = false
+        podman.enabled = false
+        charliecloud.enabled = false
+        apptainer.enabled = false
+    }
+    charliecloud {
+        charliecloud.enabled = true
+        conda.enabled = false
+        docker.enabled = false
+        singularity.enabled = false
+        podman.enabled = false
+        shifter.enabled = false
+        apptainer.enabled = false
+    }
+    apptainer {
+        apptainer.enabled = true
+        apptainer.autoMounts = true
+        conda.enabled = false
+        docker.enabled = false
+        singularity.enabled = false
+        podman.enabled = false
+        shifter.enabled = false
+        charliecloud.enabled = false
+    }
+}
 
 env {
     R_PROFILE_USER   = "/.Rprofile"