After the last changes to introduce the generation of HTML reports, a bug was introduced that prevents the workflow engine from submitting the actual jobs.
It seems that the report flag just generates the HTML based on the Snakefile and returns True if everything went fine, but it doesn't schedule the rules.
After the last changes to introduce the generation of HTML reports, a bug was introduced that prevents the workflow engine from submitting the actual jobs.
It seems that the report flag just generates the HTML based on the Snakefile and returns
Trueif everything went fine, but it doesn't schedule the rules.https://github.com/snakemake/snakemake/blob/26373e66fbaba04fa076aebb24ad869f41f228b9/snakemake/workflow.py#L872-L876
To fix it we can call the
snakemake()once again, passing thereportflag so it also takes into account start/end times to build a richer report.