From 090ce07a19800bd7885bc4feb598005852855a6e Mon Sep 17 00:00:00 2001
From: Xichen Wu <102925032+wxicu@users.noreply.github.com>
Date: Wed, 7 Feb 2024 16:09:44 +0100
Subject: [PATCH] Update test_action.yml

---
 .github/workflows/test_action.yml | 30 +++++++++++++++++++++++++++---
 1 file changed, 27 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/test_action.yml b/.github/workflows/test_action.yml
index 85c3a7e..d455996 100644
--- a/.github/workflows/test_action.yml
+++ b/.github/workflows/test_action.yml
@@ -1,8 +1,8 @@
 name: hadge test workflow
 on: push
 jobs:
-  test:
-    name: Run pipeline with test data
+  test_genetic:
+    name: Run pipeline in genetic mode with test data
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
@@ -24,4 +24,28 @@ jobs:
         run: bash ${GITHUB_WORKSPACE}/test_data/download_data.sh
       - name: Run pipeline with test data
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,conda --souporcell False --generate_anndata False
+          nextflow run ${GITHUB_WORKSPACE} -profile test,conda --mode genetic --souporcell False --generate_anndata False
+test_hashing:
+    name: Run pipeline in hashing mode with test data
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v3
+      - name: Setup conda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          miniconda-version: "latest"
+          channels: conda-forge, bioconda
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@v1
+      - name: Set up Python to install gdown
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.9"
+          cache: "pip"
+      - name: Download test dataset
+        run: bash ${GITHUB_WORKSPACE}/test_data/download_data.sh
+      - name: Run pipeline with test data
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test,conda --mode hashing --generate_anndata False