From b248b5dc2aa13b8d81cb30c34e9b5e18082ab20c Mon Sep 17 00:00:00 2001
From: RAHenriksen <rah@hotmail.dk>
Date: Thu, 24 Oct 2024 14:02:00 +0200
Subject: [PATCH] altered conda environment

---
 .github/workflows/cdiff_fbi_workflow.yml |  9 +++------
 environment.yml                          | 17 +++++++++++++++++
 2 files changed, 20 insertions(+), 6 deletions(-)
 create mode 100644 environment.yml

diff --git a/.github/workflows/cdiff_fbi_workflow.yml b/.github/workflows/cdiff_fbi_workflow.yml
index c3871d3..4cfdd86 100644
--- a/.github/workflows/cdiff_fbi_workflow.yml
+++ b/.github/workflows/cdiff_fbi_workflow.yml
@@ -27,14 +27,11 @@ jobs:
         uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
+          environment-file: environment.yml
+          activate-environment: cdiff_pipeline
           python-version: ${{ matrix.python-version }}
 
-      # step 3: Create the conda environment manually
-      - name: Create conda environment
-        run: |
-          conda create --name cdiff_pipeline picard gatk4 biopython ruamel.yaml kraken bwa samtools
-
-      # step 4
+      # step 3
       - name: Run test script
         run: |
           conda activate cdiff_pipeline
diff --git a/environment.yml b/environment.yml
new file mode 100644
index 0000000..b74476c
--- /dev/null
+++ b/environment.yml
@@ -0,0 +1,17 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - python=3.11
+  - picard
+  - gatk4
+  - kraken
+  - bwa 
+  - samtools
+  - ruamel.yaml
+  - git
+  - pip
+  - pip:
+      - biopython
+      - pytest
\ No newline at end of file