From 53c41a372e3f462b6fce33075cd74d9430b88ce4 Mon Sep 17 00:00:00 2001 From: Jover Lee Date: Mon, 17 Jun 2024 16:38:47 -0700 Subject: [PATCH] Add `benchmark` to the Snakemake style guide Makes it so much easier to identify bottlenecks in workflows if they all just start out with benchmarks! --- src/reference/snakemake-style-guide.rst | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/src/reference/snakemake-style-guide.rst b/src/reference/snakemake-style-guide.rst index 4db75316..074890d5 100644 --- a/src/reference/snakemake-style-guide.rst +++ b/src/reference/snakemake-style-guide.rst @@ -227,3 +227,10 @@ Run workflows with ``--show-failed-logs`` Run workflows with the ``--show-failed-logs`` which will print the logs for failed jobs to the terminal when the workflow exits. This pattern helps users identify error messages without first finding the corresponding log file. + +Always use the ``benchmark`` directive +====================================== + +Use `the Snakemake benchmark directive `_ +for each rule so that it is easy to track run time and memory usage. +This makes it easier for us identify bottlenecks in workflows without parsing Snakemake logs.