From 7f7c630dd8c4b2ef6eba5553fed099460340c7a1 Mon Sep 17 00:00:00 2001
From: dweemx <maxime.dewaegeneer@kuleuven.vib.be>
Date: Mon, 22 Mar 2021 12:53:41 +0100
Subject: [PATCH] [scanpy] Add multi-sample QC workflow

---
 main.nf            | 29 +++++++++++++++++++++++---
 src/scanpy/main.nf | 52 +++++++++++++++++++++++++++++++++++++++-------
 2 files changed, 71 insertions(+), 10 deletions(-)

diff --git a/main.nf b/main.nf
index 139a42e2..b822f8e4 100644
--- a/main.nf
+++ b/main.nf
@@ -273,15 +273,15 @@ workflow single_sample_qc {
 
     include {
         single_sample_qc as SINGLE_SAMPLE_QC;
-    } from './main' params(params)
+    } from './src/scanpy/main' params(params)
     include {
-        PUBLISH as PUBLISH_SINGLE_SAMPLE_SCOPE;
+        PUBLISH;
     } from "./src/utils/workflows/utils" params(params)
 
     getDataChannel | SINGLE_SAMPLE_QC
 
     if(params.utils?.publish) {
-        PUBLISH_SINGLE_SAMPLE_SCOPE(
+        PUBLISH(
             SINGLE_SAMPLE_QC.out.filtered,
             "SINGLE_SAMPLE_QC",
             "h5ad",
@@ -292,6 +292,29 @@ workflow single_sample_qc {
 
 }
 
+workflow multi_sample_qc {
+
+    include {
+        multi_sample_qc as MULTI_SAMPLE_QC;
+    } from './src/scanpy/main' params(params)
+    include {
+        PUBLISH;
+    } from "./src/utils/workflows/utils" params(params)
+
+    getDataChannel | MULTI_SAMPLE_QC
+
+    if(params.utils?.publish) {
+        PUBLISH(
+            MULTI_SAMPLE_QC.out.filtered,
+            "MULTI_SAMPLE_QC",
+            "h5ad",
+            null,
+            false
+        )
+    }  
+
+}
+
 workflow multi_sample {
 
     include {
diff --git a/src/scanpy/main.nf b/src/scanpy/main.nf
index e0e10ff9..2d93a789 100644
--- a/src/scanpy/main.nf
+++ b/src/scanpy/main.nf
@@ -6,14 +6,19 @@ import static groovy.json.JsonOutput.*
 
 //////////////////////////////////////////////////////
 //  Import sub-workflows from the modules:
-
+include {
+    getBaseName;
+} from '../utils/processes/files.nf'
+include {
+    FILTER_AND_ANNOTATE_AND_CLEAN;
+} from '../utils/workflows/filterAnnotateClean.nf' params(params)
 include { 
     INIT;
-    getDataChannel;
 } from '../utils/workflows/utils' params(params)
 INIT(params)
 include {
-    SC__FILE_CONVERTER
+    SC__FILE_CONVERTER;
+    SC__FILE_CONCATENATOR;
 } from '../utils/processes/utils' params(params)
 include {
     getDataChannel
@@ -25,7 +30,6 @@ include {
     SINGLE_SAMPLE
 } from './workflows/single_sample.nf' params(params)
 
-
 workflow single_sample {
 
     main:
@@ -38,9 +42,43 @@ workflow single_sample {
 
 workflow single_sample_qc {
 
+    take:
+        data
+
     main:
-        getDataChannel | \
-            SC__FILE_CONVERTER | \
-            QC_FILTER
+        out = SC__FILE_CONVERTER( data )
+        out = FILTER_AND_ANNOTATE_AND_CLEAN( out )
+        QC_FILTER( out )
 
 }
+
+workflow multi_sample_qc {
+
+    take:
+        data
+
+    main:
+        if(!params?.sc?.scanpy?.filter) {
+            throw new Exception("VSN ERROR: Missing params.sc.scanpy.filter config.")
+        }
+        if(!params?.sc?.file_concatenator) {
+            throw new Exception("VSN ERROR: Missing params.sc.file_concatenator config.")
+        }
+
+        out = data | \
+            SC__FILE_CONVERTER | \
+            FILTER_AND_ANNOTATE_AND_CLEAN
+
+        out = QC_FILTER( out ).filtered
+        out = SC__FILE_CONCATENATOR( 
+            out.map {
+                it -> it[1]
+            }.toSortedList( 
+                { a, b -> getBaseName(a, "SC") <=> getBaseName(b, "SC") }
+            )
+        )
+
+    emit:
+        filtered = out
+
+}
\ No newline at end of file