HaplotypeCaller is running with the check_contamination.done file

[brcopeland]

There must be some bug in https://github.com/brcopeland/wxs_pipeline/blob/83a775a05c14a4933e0d786b4e16423210dbe36d/%7B%7Bcookiecutter.project_name%7D%7D/workflow/Snakefile#L208, but I'm rather confused as to what the problem is...

[brcopeland]

I reported the underlying issue and what I believe is a fix in https://github.com/snakemake/snakemake/issues/55.

[brcopeland]

This is unfortunately still an issue (that confusingly only occurs some of the time). It also occurs in the mark_duplicates and merge_read_group_bams (but only sometimes) as these rely on this aggregate function. Some of the time when snakemake encounters a checkpoints...get() call the function short-circuits and just returns the value of that call (which is certainly not intended and very weird).

So current workarounds until this gets fixed by the snakemake developers:

• return the list of files to be aggregated without using a checkpoint
• run the affected rules locally (i.e. by running an interactive cluster job and then running snakemake locally there)
• try running snakemake again (again the bug only happens some of the time)