From 666467da42372a14495cd2f8a79953cd6191ccd5 Mon Sep 17 00:00:00 2001
From: Chengxin Dai <37200167+daichengxin@users.noreply.github.com>
Date: Sun, 14 Jan 2024 00:15:39 +0800
Subject: [PATCH] library creation

---
 nextflow.config      | 11 +++++++----
 nextflow_schema.json | 13 +++++++++++++
 workflows/dia.nf     |  6 +++++-
 3 files changed, 25 insertions(+), 5 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index 7182f12e..7978011d 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -174,10 +174,13 @@ params {
     species_genes           = false
     diann_normalize         = true
     diann_speclib           = null
-    
-    /// DIA-NN: Extras
-    skip_preliminary_analysis = false
-    empirical_assembly_log = null
+
+    // DIA-NN: Extras
+    skip_preliminary_analysis    = false
+    empirical_assembly_log       = null
+    random_preanalysis           = false
+    empirical_assembly_ms_n      = 200
+
 
     // MSstats general options
     msstats_remove_one_feat_prot    = true
diff --git a/nextflow_schema.json b/nextflow_schema.json
index c8574be9..f70e01b3 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -967,6 +967,19 @@
                     "description": "Enable cross-run normalization between runs by diann.",
                     "default": true,
                     "fa_icon": "far fa-check-square"
+                },
+                "random_preanalysis": {
+                    "type": "boolean",
+                    "description": "Enable random selection of spectrum files to generate empirical library.",
+                    "default": false,
+                    "fa_icon": "far fa-check-square"
+                },
+                "empirical_assembly_ms_n": {
+                    "type": "integer",
+                    "description": "The number of randomly selected spectrum files.",
+                    "default": 200,
+                    "fa_icon": "fas fa-filter",
+                    "hidden": true
                 }
             },
             "fa_icon": "fas fa-braille"
diff --git a/workflows/dia.nf b/workflows/dia.nf
index 0f703620..69bc2538 100644
--- a/workflows/dia.nf
+++ b/workflows/dia.nf
@@ -75,7 +75,11 @@ workflow DIA {
         //
         // MODULE: DIANN_PRELIMINARY_ANALYSIS
         //
-        DIANN_PRELIMINARY_ANALYSIS(ch_file_preparation_results.combine(speclib))
+        if (params.random_preanalysis){
+            DIANN_PRELIMINARY_ANALYSIS(ch_file_preparation_results.randomSample(params.empirical_assembly_ms_n, 2024).combine(speclib))
+        } else{
+            DIANN_PRELIMINARY_ANALYSIS(ch_file_preparation_results.combine(speclib))
+        }
         ch_software_versions = ch_software_versions
             .mix(DIANN_PRELIMINARY_ANALYSIS.out.version.ifEmpty(null))