From 9c30059c5573a5077b152794b30a6e9dbe4d92e7 Mon Sep 17 00:00:00 2001
From: KrisDavie <kristofer.davie@kuleuven.vib.be>
Date: Mon, 6 Jul 2020 09:01:41 +0200
Subject: [PATCH] Add harmony only workflow and config

---
 main.nf         | 21 ++++++++++++++++++++-
 nextflow.config |  4 ++++
 src/harmony     |  2 +-
 3 files changed, 25 insertions(+), 2 deletions(-)

diff --git a/main.nf b/main.nf
index b53bae8f..62d6a6f9 100644
--- a/main.nf
+++ b/main.nf
@@ -76,6 +76,26 @@ workflow harmony {
 
 }
 
+workflow harmony_only {
+
+    include {
+        BEC_HARMONY as HARMONY;
+    } from './src/harmony/workflows/harmony_only' params(params)
+    include {
+        PUBLISH as PUBLISH_HARMONY;
+    } from "./src/utils/workflows/utils" params(params)
+
+    getDataChannel | HARMONY
+    PUBLISH_HARMONY(
+        HARMONY.out,
+        "HARMONY",
+        "h5ad",
+        null,
+        false
+    )
+
+}
+
 // run multi-sample with bbknn, then scenic from the filtered output:
 workflow bbknn_scenic {
 
@@ -566,4 +586,3 @@ workflow sra_cellranger_bbknn_scenic {
     )    
 
 }
-
diff --git a/nextflow.config b/nextflow.config
index 44bd8066..5171a040 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -94,6 +94,10 @@ profiles {
             includeConfig 'src/harmony/harmony.config'
         }
     }
+    harmony_only {
+        includeConfig 'src/scanpy/scanpy.config'
+        includeConfig 'src/harmony/harmony.config'
+    }
     bbknn_scenic {
         includeConfig 'src/scanpy/scanpy.config'
         includeConfig 'src/scanpy/conf/bbknn.config'
diff --git a/src/harmony b/src/harmony
index 41dc66be..87bd20db 160000
--- a/src/harmony
+++ b/src/harmony
@@ -1 +1 @@
-Subproject commit 41dc66be2c6bfabc829d569672615aee1fbaf00d
+Subproject commit 87bd20db8b4d6619f2a4a54288b38c1f33add2de