Add harmony only workflow and config

vib-singlecell-nf · Jul 6, 2020 · 9c30059 · 9c30059
1 parent 9e52a96
commit 9c30059
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Showing 3 changed files with 25 additions and 2 deletions.
diff --git 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
@@ -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
+4 −1		workflows/bec_harmony.nf
+32 −0		workflows/harmony_only.nf