feat(config): SLURM job-array submission for per-sample fan-out stages

conf/modules.config

@@ -18,6 +18,15 @@ process {
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
 
+    // Per-sample fan-out stages benefit from SLURM job-array submission so a
+    // multi-sample run counts as one job for fair-share priority. The `array`
+    // directive is only honoured by executors that support it (SLURM, LSF, …);
+    // gate on params.slurm so the local / standard executor sees array = 0
+    // (a no-op) and never tries to submit an array.
+    withName: 'DRAM:ANNOTATE:CALL:.*|DRAM:ANNOTATE:DB_SEARCH:.*|DRAM:ANNOTATE:QC:COLLECT.*' {
+        array = params.slurm ? params.array_size : 0
+    }
+
     withName: 'MULTIQC' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [

nextflow.config

@@ -182,6 +182,11 @@ params {
 
     /* Process Options */
     queue_size = 10
+    // SLURM (or other supporting executor) job-array submission for the
+    // heavy per-sample fan-out stages: CALL/DB_SEARCH/QC:COLLECT_*.
+    // 0 disables (default) so a fresh user with the local executor isn't
+    // surprised. Set when running with --slurm.
+    array_size = 0
     // This is the resource requirements for a single process
     // Not the limit to the total resources available to the pipeline
     // Up to queue_size processes can run in parallel, of various sizes

nextflow_schema.json

@@ -690,6 +690,11 @@
                     "type": "integer",
                     "default": 10,
                     "description": "Maximum number of jobs to submit to the queue at once."
+                },
+                "array_size": {
+                    "type": "integer",
+                    "default": 0,
+                    "description": "Number of tasks to submit per SLURM job array. 0 disables (default) so the local executor is unaffected. Set when running with --slurm."
                 }
             }
         },