From 25fd3a9117b763fa0fc71ffbbe064eb6d2ea9db1 Mon Sep 17 00:00:00 2001
From: Ivan Blagoev Topolsky <ivan.topolsky@bsse.ethz.ch>
Date: Wed, 27 Dec 2023 18:37:24 +0100
Subject: [PATCH] temporary workaround for snakemake 8's breaking changes

---
 Dockerfile                       | 3 ++-
 tests/conda_snakedeploy_env.yaml | 2 +-
 tests/conda_test_env.yaml        | 2 +-
 utils/quick_install.sh           | 3 ++-
 4 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index f9e52d43..ac60e1e8 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -12,7 +12,8 @@ ARG vpipe_path=${install_path}/V-pipe
 ARG envs_path=${install_path}/conda_envs
 ARG test_data=/test-data
 ARG virus_download_list
-ARG snaketag=stable
+# HACK Snakemake v8 has breaking changes
+ARG snaketag=v7.32.4
 
 ###
 ### Stage 0: download conda environments
diff --git a/tests/conda_snakedeploy_env.yaml b/tests/conda_snakedeploy_env.yaml
index 3f8172ca..ce615fae 100644
--- a/tests/conda_snakedeploy_env.yaml
+++ b/tests/conda_snakedeploy_env.yaml
@@ -4,6 +4,6 @@ channels:
   - bioconda
 dependencies:
   - python <3.12 # temporary fix for snakemake issue #2480
-  - snakemake-minimal
+  - snakemake-minimal <8 # HACK Snakemake v8 has breaking changes
   - snakedeploy
   - go-yq
diff --git a/tests/conda_test_env.yaml b/tests/conda_test_env.yaml
index 7c0122b8..e852d1b3 100644
--- a/tests/conda_test_env.yaml
+++ b/tests/conda_test_env.yaml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   #- defaults # see: https://github.com/conda-forge/status/issues/144
 dependencies:
-  - snakemake-minimal
+  - snakemake-minimal <8 # HACK Snakemake v8 has breaking changes
diff --git a/utils/quick_install.sh b/utils/quick_install.sh
index a51e9941..207677fb 100755
--- a/utils/quick_install.sh
+++ b/utils/quick_install.sh
@@ -176,7 +176,8 @@ conda config --set channel_priority strict
 # NOTE conda-forge *HAS TO* be higher than bioconda
 
 VPIPEENV=
-if mamba install --yes snakemake-minimal mamba $GIT; then	# NOTE Mac OS X and some Linux dockers don't have git out of the box
+# HACK Snakemake v8 has breaking changes
+if mamba install --yes 'snakemake-minimal<8' mamba $GIT; then	# NOTE Mac OS X and some Linux dockers don't have git out of the box
 	: # success!
 else
 	oops 'I cannot install snakemake in base environment. Conflicts ?'