Merge pull request #341 from daichengxin/dev

library creation
bigbio · Jan 13, 2024 · e9ae266 · e9ae266
2 parents eb6985f + 666467d
commit e9ae266
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Showing 3 changed files with 25 additions and 5 deletions.
diff --git 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
@@ -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
@@ -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))