From ed21adba972047a8ff155307799434d8a2a6cddb Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 8 Dec 2025 22:02:46 +0000
Subject: [PATCH 1/4] Initial plan


From 7f6ef0331cc6f35f54930bec05cd66ec95ad23df Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 8 Dec 2025 22:05:28 +0000
Subject: [PATCH 2/4] Update CI workflow to use conda/miniforge for dependency
 installation

Co-authored-by: tseemann <453972+tseemann@users.noreply.github.com>
---
 .github/workflows/main.yml | 15 +++++++++++++--
 1 file changed, 13 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 3219865..6229f24 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -10,16 +10,26 @@ jobs:
     - name: Checkout code
       uses: actions/checkout@v4
 
+    - name: Setup Miniforge
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        miniforge-version: latest
+        activate-environment: snippy-env
+        channels: conda-forge,bioconda,defaults
+        channel-priority: strict
+
     - name: Install Dependencies
+      shell: bash -el {0}
       run: |
-        sudo apt-get update
-        sudo apt-get install -y libstdc++6 liblzma5 libbz2-1.0 bioperl samtools freebayes bcftools
+        conda install -y samtools bcftools freebayes bedtools bwa minimap2 parallel vcflib vt snpeff seqtk snp-sites wgsim any2fasta perl-bioperl samclip
 
     - name: Add binaries to PATH
+      shell: bash -el {0}
       run: |
         echo "$PWD/bin:$PWD/binaries/noarch:$PWD/binaries/linux" >> $GITHUB_PATH
 
     - name: Check snippy versions and configurations
+      shell: bash -el {0}
       run: |
         snippy --version
         snippy --check
@@ -27,6 +37,7 @@ jobs:
         snippy-core --check
 
     - name: Run tests
+      shell: bash -el {0}
       run: |
         make -C test
 

From ee9d57d97539e2896d23601ab0665ee4e0c9491b Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 8 Dec 2025 22:06:32 +0000
Subject: [PATCH 3/4] Improve readability of conda install command with
 multi-line format

Co-authored-by: tseemann <453972+tseemann@users.noreply.github.com>
---
 .github/workflows/main.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 6229f24..62cbe7a 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -21,7 +21,11 @@ jobs:
     - name: Install Dependencies
       shell: bash -el {0}
       run: |
-        conda install -y samtools bcftools freebayes bedtools bwa minimap2 parallel vcflib vt snpeff seqtk snp-sites wgsim any2fasta perl-bioperl samclip
+        conda install -y \
+          samtools bcftools freebayes bedtools \
+          bwa minimap2 parallel vcflib vt snpeff \
+          seqtk snp-sites wgsim any2fasta \
+          perl-bioperl samclip
 
     - name: Add binaries to PATH
       shell: bash -el {0}

From d806a778e290a25808259de2cbe018bca9cf5128 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 8 Dec 2025 22:07:18 +0000
Subject: [PATCH 4/4] Remove defaults channel to avoid package conflicts

Co-authored-by: tseemann <453972+tseemann@users.noreply.github.com>
---
 .github/workflows/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 62cbe7a..ae67c99 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -15,7 +15,7 @@ jobs:
       with:
         miniforge-version: latest
         activate-environment: snippy-env
-        channels: conda-forge,bioconda,defaults
+        channels: conda-forge,bioconda
         channel-priority: strict
 
     - name: Install Dependencies