remove separate snpit container and fix parenthesis in config

Author: taranewman

environments/snpit_container.yml

@@ -60,6 +60,8 @@ profiles {
 	    conda.cacheDir = params.cache
 	}
 
+    }
+
     apptainer {
     	apptainer.enabled = true
 	    process.container = "oras://ghcr.io/bccdc-phl/tbprofiler-nf:9e89d28e3de50f49"
@@ -68,7 +70,6 @@ profiles {
 	    }
     }
 
-    }
 }
 
 process {
@@ -82,3 +83,20 @@ trace {
     overwrite = true
     file = "${params.outdir}/nextflow_trace.tsv"
 }
+
+
+process {
+    withName: snpit {
+
+    conda = "$baseDir/environments/snpit.yml"
+	container = "oras://ghcr.io/bccdc-phl/snpit-container:63179e326beaaeaa"
+
+    }
+ 
+	withName: plot_coverage {
+
+    conda = "$baseDir/environments/bakta.yml"
+	container = "oras://ghcr.io/bccdc-phl/ghcr.io/bccdc-phl/seaborn:1e75cc4939fa0e57"
+
+    }
+}