From e5c36087c1aef83dcef7200b88a139d4ad15f4a8 Mon Sep 17 00:00:00 2001
From: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>
Date: Fri, 16 Aug 2024 13:37:54 +0200
Subject: [PATCH] Fix pbmc test resources after #748 (#861)

---
 resources_test_scripts/pbmc_1k_protein_v3.sh | 13 +++++++++++++
 src/integrate/harmonypy/test.py              |  2 +-
 src/neighbors/bbknn/test.py                  |  4 ++--
 3 files changed, 16 insertions(+), 3 deletions(-)

diff --git a/resources_test_scripts/pbmc_1k_protein_v3.sh b/resources_test_scripts/pbmc_1k_protein_v3.sh
index cf12c4b4544..389e43b9f1e 100755
--- a/resources_test_scripts/pbmc_1k_protein_v3.sh
+++ b/resources_test_scripts/pbmc_1k_protein_v3.sh
@@ -99,6 +99,19 @@ nextflow \
   --obs_covariates sample_id \
   -resume
 
+# run integration
+nextflow \
+  run . \
+  -main-script target/nextflow/workflows/integration/harmony_leiden/main.nf \
+  -c src/workflows/utils/labels_ci.config \
+  -profile docker \
+  --id pbmc_1k_protein_v3_mms_integration \
+  --input "${OUT}_mms.h5mu" \
+  --output "`basename $OUT`_mms.h5mu" \
+  --publishDir `dirname $OUT` \
+  --obs_covariates sample_id \
+  -resume
+
 python <<HEREDOC
 import mudata as mu
 mudata = mu.read_h5mu("${DIR}/pbmc_1k_protein_v3_filtered_feature_bc_matrix.h5mu")
diff --git a/src/integrate/harmonypy/test.py b/src/integrate/harmonypy/test.py
index 25afbaf691f..7eab3f7649b 100644
--- a/src/integrate/harmonypy/test.py
+++ b/src/integrate/harmonypy/test.py
@@ -21,7 +21,7 @@ def test_harmonypy(run_component, tmp_path):
         "--modality", "rna",
         "--obsm_input", "X_pca",
         "--obsm_output", "X_pca_int",
-        "--obs_covariates", "leiden",
+        "--obs_covariates", "harmony_integration_leiden_1.0",
         "--output", str(output_path),
         "--output_compression", "gzip"])
     assert output_path.is_file()
diff --git a/src/neighbors/bbknn/test.py b/src/neighbors/bbknn/test.py
index 5500f87a960..9a6418ff901 100644
--- a/src/neighbors/bbknn/test.py
+++ b/src/neighbors/bbknn/test.py
@@ -41,7 +41,7 @@ def test_simple_integration(run_component, tmp_path, sample_mudata):
     run_component([
         "--input", str(tmp_input_path),
         "--output", str(output_path),
-        "--obs_batch", "leiden",
+        "--obs_batch", "harmony_integration_leiden_1.0",
         "--obsm_input", "X_pca",
         "--output_compression", "gzip"
     ])
@@ -59,7 +59,7 @@ def test_alternative_names(run_component, tmp_path, sample_mudata):
     run_component([
         "--input", str(tmp_input_path),
         "--output", str(output_path),
-        "--obs_batch", "leiden",
+        "--obs_batch", "harmony_integration_leiden_1.0",
         "--obsm_input", "X_pca",
         "--output_compression", "gzip",
         "--uns_output", "my_neighbors",