Let's say I have a snakemake rule something like this
rule xxx:
output:
temp(directory("atac_seq/"))
shell:
"""
snakemake --cores all
"""
and in my config file, I have an config["delete"] = #True or False
Can I make temp delete atac_seq based on whether delete is true or false?
e.g.
rule xxx:
output:
if config["delete"] = True:
temp(directory("atac_seq/"))
elif config["delete"] = False:
directory("atac_seq/")
shell:
"""
snakemake --cores all
"""
I can't think of a way to do this other than adding rm in shell.
Rather than trying to encode this in your workflow, maybe you are better off just using the --notemp flag when running Snakmake. This will keep all the temporary files and you don't have to put any extra code in your Snakefile. You can then later use --delete-temp-output if you want to clean up all the temp files.
If you really do want to achieve what you sketched out above, it's do-able. Since temp() is just a function you can wrap it in another function.
def mytemp(filename):
if config['delete']:
return temp(filename)
else:
return filename
rule xxx:
output:
mytemp(directory("foo"))
shell:
"""
mkdir {output} ; touch {output}/foo.out
"""
I am a bit alarmed that you are calling snakemake from a snakemake rule. This is generally a bad idea and leads to locking issues as well as scrambled output on the screen. I'd generally just use a wrapper shell script, or maybe you just need a profile here to set the --cores all setting.