Restructure pipeline configs to improve discoverability

CLAUDE.md

@@ -0,0 +1,14 @@
+# How this repo is used currently
+
+In each nf-core con or pipeline, these lines are included. So basically, nf-core custom.config and the pipeline rnaseq.config will get pulled in.
+
+```nextflow
+// Load nf-core custom profiles from different institutions
+
+// If params.custom_config_base is set AND either the NXF_OFFLINE environment variable is not set or params.custom_config_base is a local path, the nfcore_custom.config file from the specified base path is included.
+// Load nf-core/rnaseq custom profiles from different institutions.
+includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
+
+// Load nf-core/rnaseq custom profiles from different institutions.
+includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/pipeline/rnaseq.config" : "/dev/null"
+```

nfcore_custom.config

@@ -374,7 +374,7 @@ profiles {
         includeConfig "${params.custom_config_base}/conf/uod_hpc.config"
     }
     uppmax {
-        includeConfig "${params.custom_config_base}/conf/uppmax.config"
+        includeConfig "${params.custom_config_base}/conf/uppmax/nextflow.config"
     }
     utd_ganymede {
         includeConfig "${params.custom_config_base}/conf/utd_ganymede.config"