From 2e08240ecb78e4c6a0b56547b902c92bb7550b03 Mon Sep 17 00:00:00 2001
From: Christian Meesters <meesters@uni-mainz.de>
Date: Tue, 27 Aug 2024 12:27:39 +0200
Subject: [PATCH 1/2] feat: added flag to cancel all jobs upon a failure of one

---
 snakemake_executor_plugin_slurm/__init__.py | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/snakemake_executor_plugin_slurm/__init__.py b/snakemake_executor_plugin_slurm/__init__.py
index a39936b1..656e7e66 100644
--- a/snakemake_executor_plugin_slurm/__init__.py
+++ b/snakemake_executor_plugin_slurm/__init__.py
@@ -40,6 +40,18 @@ class ExecutorSettings(ExecutorSettingsBase):
             "required": False,
         },
     )
+    cancel_workflow_upon_failure: bool = field(
+        default=False,
+        metadata={
+            "help": """
+                    Negates the `--keep-going` flag in Snakemake.
+                    If set to True, the entire workflow will be canceled
+                    upon recognition of a failed job.
+                    """,
+            "env_var": False,
+            "required": False,
+        },
+    )
 
 
 # Required:
@@ -373,6 +385,8 @@ async def check_active_jobs(
                     )
                     self.report_job_error(j, msg=msg, aux_logs=[j.aux["slurm_logfile"]])
                     active_jobs_seen_by_sacct.remove(j.external_jobid)
+                    if self.settings.cancel_workflow_upon_failure:
+                        self.cancel_jobs(active_jobs)
                 else:  # still running?
                     yield j
 

From db746012e7f047a1e4ce0e1e39300ba7006cc185 Mon Sep 17 00:00:00 2001
From: Christian Meesters <meesters@uni-mainz.de>
Date: Tue, 27 Aug 2024 13:24:07 +0200
Subject: [PATCH 2/2] docs: complemented docs to accomodate for the previous
 commit

---
 docs/further.md | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/docs/further.md b/docs/further.md
index 96fea95a..acb585b5 100644
--- a/docs/further.md
+++ b/docs/further.md
@@ -31,8 +31,6 @@ Usually, it is advisable to persist such settings via a
 [configuration profile](https://snakemake.readthedocs.io/en/latest/executing/cli.html#profiles), which
 can be provided system-wide, per user, and in addition per workflow.
 
-The executor waits per default 40 seconds for its first check of the job status. Using `--slurm-init-seconds-before-status-checks=<time in seconds>` this behaviour can be altered.
-
 ## Ordinary SMP jobs
 
 Most jobs will be carried out by programs that are either single-core
@@ -181,6 +179,12 @@ rule myrule:
 
 Again, rather use a [profile](https://snakemake.readthedocs.io/en/latest/executing/cli.html#profiles) to specify such resources.
 
+## Configuring Run Time Behaviour
+
+The executor waits per default 40 seconds for its first check of the job status. Using `--slurm-init-seconds-before-status-checks=<time in seconds>` this behaviour can be altered.
+
+Snakemake will abort local runs upon failure. Using the `--keep-going` flag, Snakemake will proceed to submit independent jobs, if a job fails. This plugin offers an additional flag to cancel the entire workflow, when a job fails - this might be helpful during development: `--slurm-cancel-workflow-upon-failure`. Note, that you can use `--rerun-incomplete`/`--ri` to proceed after a failed workflow (and fixing parameters), as usual.
+
 ## Software Recommendations
 
 ### Conda, Mamba