Add IRIS reference config and fix config load order

- Create conf/mskcc_refs.config with IRIS reference_base path
- Move references.config include into iris/juno profiles (after
  base paths are set) so params.genome_base resolves correctly
- Add overwrite=true to trace/report/timeline/dag directives
- Remove juno.config dependency from iris profile

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: johnoooh

conf/mskcc_refs.config

@@ -0,0 +1,15 @@
+/*
+ * -------------------------------------------------
+ * IRIS config
+ * -------------------------------------------------
+ * Pipeline parameters specific to running Tempo on
+ * the IRIS HPC cluster at MSKCC (SLURM + Singularity)
+ * -------------------------------------------------
+ */
+
+params {
+  max_memory = "128.GB"
+  reference_base = "/data1/core006/ccs_pipelines/pipeline_resources/"
+  targets_base   = "${reference_base}/mskcc-igenomes/${(params.genome ?: 'GRCh37').toLowerCase()}/tempo_targets"
+  genome_base = params.genome == 'GRCh37' ? "${reference_base}/mskcc-igenomes/igenomes/Homo_sapiens/GATK/GRCh37" : params.genome == 'GRCh38' ? "${reference_base}/mskcc-igenomes/igenomes/Homo_sapiens/GATK/GRCh38" : "${reference_base}/mskcc-igenomes/igenomes/smallGRCh37"
+}

nextflow.config

@@ -185,9 +185,6 @@ includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${pa
 // Load modules.config for DSL2 module specific options
 includeConfig 'conf/modules.config'
 
-// Load Tempo reference genome definitions (params.genomes map)
-// These are resolved to flat nf-core params (params.fasta, etc.) in main.nf
-includeConfig 'conf/references.config'
 
 profiles {
     debug {
@@ -296,6 +293,7 @@ profiles {
     juno {
         // MSKCC Juno HPC cluster config
         includeConfig 'conf/juno.config'
+        includeConfig 'conf/references.config'
         includeConfig 'conf/slurm.config'
         singularity.enabled     = true
         singularity.autoMounts  = true
@@ -305,8 +303,8 @@ profiles {
         // MSKCC IRIS HPC cluster config
         // Uses nf-core institutional config from https://github.com/nf-core/configs
         // See: https://nf-co.re/configs/iris
-        // Load MSKCC reference paths (user must set reference_base in juno.config or CLI)
-        includeConfig 'conf/juno.config'
+        includeConfig 'conf/mskcc_refs.config'
+        includeConfig 'conf/references.config'
     }
 }
 
@@ -334,20 +332,24 @@ nextflow.enable.configProcessNamesValidation = false
 
 def trace_timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss')
 timeline {
-    enabled = true
-    file    = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
+    enabled   = true
+    overwrite = true
+    file      = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
 }
 report {
-    enabled = true
-    file    = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
+    enabled   = true
+    overwrite = true
+    file      = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
 }
 trace {
-    enabled = true
-    file    = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
+    enabled   = true
+    overwrite = true
+    file      = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
 }
 dag {
-    enabled = true
-    file    = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
+    enabled   = true
+    overwrite = true
+    file      = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
 }
 
 manifest {