diff --git a/src/harmony/bin/run_harmony.R b/src/harmony/bin/run_harmony.R
index 9b3f27c7..5880a903 100755
--- a/src/harmony/bin/run_harmony.R
+++ b/src/harmony/bin/run_harmony.R
@@ -11,6 +11,10 @@ library("argparse")
 library("reticulate")
 library("anndata")
 
+# Link Python to this R session
+use_python("/opt/conda/envs/harmony-v1.0-3/bin")
+Sys.setenv(RETICULATE_PYTHON = "/opt/conda/envs/harmony-v1.0-3/bin")
+
 parser <- ArgumentParser(description='Scalable integration of single cell RNAseq data for batch correction and meta analysis')
 parser$add_argument(
     'input',
diff --git a/src/harmony/environment.yml b/src/harmony/environment.yml
index 085595fa..38de24f8 100644
--- a/src/harmony/environment.yml
+++ b/src/harmony/environment.yml
@@ -1,10 +1,11 @@
-name: harmony-v1.0-2
+name: harmony-v1.0-3
 channels:
   - r
   - conda-forge
   - bioconda
 dependencies:
   - python=3.7
+  - anndata=0.7.6
   - r-base=4.0.2
   - r-argparse=2.0.1
   - r-devtools
diff --git a/src/harmony/harmony.config b/src/harmony/harmony.config
index b4a45c73..f7781f77 100644
--- a/src/harmony/harmony.config
+++ b/src/harmony/harmony.config
@@ -1,7 +1,7 @@
 params {
     sc {
         harmony {
-            container = 'vibsinglecellnf/harmony:1.0-2'
+            container = 'vibsinglecellnf/harmony:1.0-3'
             report_ipynb = "${params.misc.test.enabled ? '../../..' : ''}/src/harmony/bin/reports/sc_harmony_report.ipynb"
             varsUse = ['batch']
             // theta = ''