From 08b80c02c19fb009c69cccc28432e640151fc6b4 Mon Sep 17 00:00:00 2001
From: vBassewitz <104062464+vBassewitz@users.noreply.github.com>
Date: Wed, 18 Dec 2024 12:56:21 +0100
Subject: [PATCH 1/4] Update entrez.yaml

enforce openssl version
---
 workflow/envs/entrez.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/workflow/envs/entrez.yaml b/workflow/envs/entrez.yaml
index 8378303d..89bf3565 100644
--- a/workflow/envs/entrez.yaml
+++ b/workflow/envs/entrez.yaml
@@ -4,3 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - entrez-direct =16.2
+  - openssl =3.4.0

From b977c77eee7c2b4173a270450b19b6e4e8caf6ff Mon Sep 17 00:00:00 2001
From: vBassewitz <104062464+vBassewitz@users.noreply.github.com>
Date: Wed, 18 Dec 2024 12:59:01 +0100
Subject: [PATCH 2/4] Update ref.smk (just for testing purpose)

added a check for openssl version
---
 workflow/rules/ref.smk | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflow/rules/ref.smk b/workflow/rules/ref.smk
index 1458b6ec..9a444d47 100644
--- a/workflow/rules/ref.smk
+++ b/workflow/rules/ref.smk
@@ -34,7 +34,7 @@ rule get_genome:
         ncbi_api_requests=1,
     shell:
         "((esearch -db nucleotide -query '{params.accession}' | "
-        "efetch -format fasta > {output}) && [ -s {output} ]) 2> {log}"
+        "efetch -format fasta > {output}) && openssl version && [ -s {output} ]) 2> {log}"
 
 
 rule get_genome_annotation:

From 663e567641f450160f7d5397b66b0633403457c1 Mon Sep 17 00:00:00 2001
From: vBassewitz <104062464+vBassewitz@users.noreply.github.com>
Date: Wed, 18 Dec 2024 13:25:15 +0100
Subject: [PATCH 3/4] Update main.yml

---
 .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 5591cf78..4ae70fb6 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -190,7 +190,7 @@ jobs:
         run: sudo df -h
 
   Benchmarks-Tests:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     env:
       GISAID_API_TOKEN: ${{ secrets.GISAID_API_TOKEN }}
     needs:

From 994ec98f44d1b71189b9b3f3ea78dd95207ad38d Mon Sep 17 00:00:00 2001
From: vBassewitz <104062464+vBassewitz@users.noreply.github.com>
Date: Wed, 18 Dec 2024 14:31:55 +0100
Subject: [PATCH 4/4] Update ref.smk

---
 workflow/rules/ref.smk | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/workflow/rules/ref.smk b/workflow/rules/ref.smk
index 9a444d47..386426d6 100644
--- a/workflow/rules/ref.smk
+++ b/workflow/rules/ref.smk
@@ -33,8 +33,8 @@ rule get_genome:
     resources:
         ncbi_api_requests=1,
     shell:
-        "((esearch -db nucleotide -query '{params.accession}' | "
-        "efetch -format fasta > {output}) && openssl version && [ -s {output} ]) 2> {log}"
+        "openssl version && ((esearch -db nucleotide -query '{params.accession}' | "
+        "efetch -format fasta > {output}) && [ -s {output} ]) 2> {log}"
 
 
 rule get_genome_annotation: