From af86bb2e68e029e9e08cdc4ac78695967f7f6599 Mon Sep 17 00:00:00 2001
From: Stephanie Yang <stephanie.yuxin.yang@gmail.com>
Date: Mon, 28 Oct 2024 16:36:26 +0100
Subject: [PATCH] Modify differential/main.nf to include limma

---
 assets/schema_tools.json                |  4 ++--
 assets/tools_samplesheet.csv            |  2 ++
 subworkflows/local/differential/main.nf | 24 ++++++++++++++++++++++++
 3 files changed, 28 insertions(+), 2 deletions(-)

diff --git a/assets/schema_tools.json b/assets/schema_tools.json
index 347a14f0..dcbbe9f8 100644
--- a/assets/schema_tools.json
+++ b/assets/schema_tools.json
@@ -12,9 +12,9 @@
             },
             "diff_method": {
                 "type": "string",
-                "errorMessage": "choose a differential analysis method (eg. deseq2, propd) or none",
+                "errorMessage": "choose a differential analysis method (eg. deseq2, limma, propd) or none",
                 "meta": ["diff_method"],
-                "enum": ["propd", "deseq2", "none"]
+                "enum": ["propd", "deseq2", "limma", "none"]
             },
             "args_diff": {
                 "type": "string",
diff --git a/assets/tools_samplesheet.csv b/assets/tools_samplesheet.csv
index 1345355a..2289918d 100644
--- a/assets/tools_samplesheet.csv
+++ b/assets/tools_samplesheet.csv
@@ -5,6 +5,8 @@ propd_grea,propd,,,,grea,
 propd_ora,propd,,,,gprofiler2,
 deseq2_gsea,deseq2,,,,gsea,
 deseq2_ora,deseq2,,,,gprofiler2,
+limma,limma,,,,,
+limma_gsea,limma,,,,gsea,
 pcorbshrink,,,propr,--metric pcor.bshrink,,
 propr,,,propr,--metric rho,,
 cor,,,propr,--metric cor,,
diff --git a/subworkflows/local/differential/main.nf b/subworkflows/local/differential/main.nf
index bd45178d..94cec0a7 100644
--- a/subworkflows/local/differential/main.nf
+++ b/subworkflows/local/differential/main.nf
@@ -3,6 +3,7 @@
 //
 include { PROPR_PROPD as PROPD } from "../../../modules/local/propr/propd/main.nf"
 include { DESEQ2_DIFFERENTIAL  } from '../../../modules/nf-core/deseq2/differential/main'
+include { LIMMA_DIFFERENTIAL } from '../../../modules/nf-core/limma/differential/main'
 
 def correct_meta_data = { meta, data, pathway ->
     def meta_clone = meta.clone() + pathway
@@ -32,6 +33,7 @@ workflow DIFFERENTIAL {
         .branch {
             propd:  it[1]["diff_method"] == "propd"
             deseq2: it[1]["diff_method"] == "deseq2"
+            limma: it[1]["diff_method"] == "limma"
         }
         .set { ch_tools_single }
 
@@ -89,6 +91,28 @@ workflow DIFFERENTIAL {
     // ch_results = ch_results
     //     .mix(DESEQ2_DIFFERENTIAL.out.results)
 
+    // ----------------------------------------------------
+    // Perform differential analysis with limma
+    // ----------------------------------------------------
+
+    ch_counts
+        .join(ch_samplesheet) //samplesheet + counts have the same meta
+        .combine(ch_contrasts) // meta is different 
+        .combine(ch_tools_single.limma) 
+        .multiMap {
+            meta_data, counts, samplesheet, meta_contrast, contrast_variable, reference, target, pathway, meta_tools ->
+                def meta = meta_data.clone() + meta_contrast.clone() + meta_tools.clone()
+                input1:  [ meta, contrast_variable, reference, target ]
+                input2:  [ meta, samplesheet, counts ]
+                pathway: [ meta, pathway ]
+        }
+        .set { ch_limma }
+
+    LIMMA_DIFFERENTIAL(ch_limma.input1.unique(), ch_limma.input2.unique())
+  
+    ch_results_genewise          = LIMMA_DIFFERENTIAL.out.results
+                                        .join(ch_limma.pathway).map(correct_meta_data).mix(ch_results_genewise)
+
     emit:
     results_pairwise          = ch_results_pairwise
     results_pairwise_filtered = ch_results_pairwise_filtered