From fa6b2b2fa667aac391d8c9eaab7641fe9746fddc Mon Sep 17 00:00:00 2001 From: Leonardo Schwarz Date: Wed, 4 Sep 2024 15:54:44 +0200 Subject: [PATCH] don't create a snakemake report --- src/depiction_targeted_preproc/pipeline/run.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/depiction_targeted_preproc/pipeline/run.py b/src/depiction_targeted_preproc/pipeline/run.py index 0ced2bd..e45aa61 100644 --- a/src/depiction_targeted_preproc/pipeline/run.py +++ b/src/depiction_targeted_preproc/pipeline/run.py @@ -31,7 +31,8 @@ def run_workflow(sample_dir: Path) -> Path: result_files = get_result_files_new(requested_artifacts=params.requested_artifacts, sample_dir=sample_dir) # invoke snakemake - SnakemakeInvoke().invoke(work_dir=sample_dir.parent, result_files=result_files) + # TODO note report file is deactivated because it's currently broken due to dependencies (jinja2) + SnakemakeInvoke(report_file=None).invoke(work_dir=sample_dir.parent, result_files=result_files) # zip the results sample_name = sample_dir.name