From 1c01b842b4648bb0cdfce20d1341c5533b559ff0 Mon Sep 17 00:00:00 2001 From: Jover Lee Date: Mon, 22 Jun 2026 11:27:37 -0700 Subject: [PATCH] Upgrade to Snakemake v9.17.0 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Mainly motivated by upgrading past v9.11.0 that no longer has fstring bug discussed in Slack.¹ We've already updated all pathogen workflows to be compatible with v9.17.0 as part of so this should not have any breaking changes. ¹ --- Dockerfile | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 4d5c1ac..25fa638 100644 --- a/Dockerfile +++ b/Dockerfile @@ -250,8 +250,9 @@ RUN python3 -m venv /usr/local/libexec/awscli \ && ln -sv /usr/local/libexec/awscli/bin/aws /usr/local/bin/aws # Install Snakemake and related optional dependencies. -# Pinned to 9.6.2 for stability (latest version on 2025-07-03) -RUN pip3 install snakemake[reports]==9.6.2 +# Pinned to 9.17.0 for stability, latest guaranteed compatible version +# based on +RUN pip3 install snakemake[reports]==9.17.0 # Snakemake plugins for remote storage providers # Pinned for stability (latest versions on 2025-07-03) RUN pip3 install snakemake-storage-plugin-http==0.3.0