feat: disable performance-heavy QC steps by default

- Set skip_dupradar=true (mostly pointless for bulk RNA-seq)
- Set skip_qualimap=true (identified as slowest QC step)
- Set skip_rseqc=true (7 resource-intensive modules by default)
- Set skip_stringtie=true (additional assembly overhead)
- Set skip_bigwig=true (coverage track generation overhead)

Follows nf-core/proposals#71 to make QC steps opt-in rather than
mandatory. Users can re-enable comprehensive QC via parameters when needed.
Significantly reduces pipeline runtime and compute costs for standard
bulk RNA-seq workflows.

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <[email protected]>
Co-Authored-By: adamrtalbot <[email protected]>

Author: 3 people

nextflow.config

@@ -89,18 +89,18 @@ params {
 
     // QC
     skip_qc                    = false
-    skip_bigwig                = false
-    skip_stringtie             = false
+    skip_bigwig                = true
+    skip_stringtie             = true
     skip_fastqc                = false
     skip_preseq                = true
-    skip_dupradar              = false
-    skip_qualimap              = false
+    skip_dupradar              = true
+    skip_qualimap              = true
     contaminant_screening      = null
     kraken_db                  = null
     save_kraken_assignments    = false
     save_kraken_unassigned     = false
     bracken_precision          = "S"
-    skip_rseqc                 = false
+    skip_rseqc                 = true
     skip_biotype_qc            = false
     skip_deseq2_qc             = false
     skip_multiqc               = false

nextflow_schema.json

@@ -677,12 +677,14 @@
                 "skip_bigwig": {
                     "type": "boolean",
                     "fa_icon": "fas fa-fast-forward",
-                    "description": "Skip bigWig file creation."
+                    "description": "Skip bigWig file creation.",
+                    "default": true
                 },
                 "skip_stringtie": {
                     "type": "boolean",
                     "fa_icon": "fas fa-fast-forward",
-                    "description": "Skip StringTie."
+                    "description": "Skip StringTie.",
+                    "default": true
                 },
                 "skip_fastqc": {
                     "type": "boolean",
@@ -698,17 +700,20 @@
                 "skip_dupradar": {
                     "type": "boolean",
                     "fa_icon": "fas fa-fast-forward",
-                    "description": "Skip dupRadar."
+                    "description": "Skip dupRadar.",
+                    "default": true
                 },
                 "skip_qualimap": {
                     "type": "boolean",
                     "fa_icon": "fas fa-fast-forward",
-                    "description": "Skip Qualimap."
+                    "description": "Skip Qualimap.",
+                    "default": true
                 },
                 "skip_rseqc": {
                     "type": "boolean",
                     "fa_icon": "fas fa-fast-forward",
-                    "description": "Skip RSeQC."
+                    "description": "Skip RSeQC.",
+                    "default": true
                 },
                 "skip_biotype_qc": {
                     "type": "boolean",