It’s not uncommon that workflows contain temporary files that should be kept for some time and then deleted once they are no longer needed. A typical case could be that some operation generates a file, which is then compressed to save space or indexed to make searching faster. There is then no need to save the original output file. Take a look at the job graph for our workflow again. The output from align_to_genome is a bam file, which contains information about all the reads for a sample and where they map in the genome. For downstream processing we need this file to be sorted by genome coordinates. This is what the rule sort_bam is for. We therefore end up with both intermediate/{sample_id}.bam and intermediate/{sample_id}.sorted.bam.

In Snakemake we can mark an output file as temporary like this:

output: temp("...")

The file will then be deleted as soon as all jobs where it’s an input have finished. Now do this for the output of align_to_genome. We have to rerun the rule for it to trigger, so use -R align_to_genome. It should look something like this:

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rule sort_bam:
    input: intermediate/SRR935090.bam
    output: intermediate/SRR935090.sorted.bam
    jobid: 2
    wildcards: sample_id=SRR935090

Removing temporary output file intermediate/SRR935090.bam.
Finished job 2.
.
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Tip
Sometimes you may want to trigger removal of temporary files without actually rerunning the jobs. You can then use the --delete-temp-output flag. In some cases you may instead want to run only parts of a workflow and therefore want to prevent files marked as temporary from being deleted (because the files are needed for other parts of the workflow). In such cases you can use the --notemp flag.

Snakemake has a number of options for marking files:

temp("..."): The output file should be deleted once it’s no longer needed by any rules.
protected("..."): The output file should be write-protected. Typically used to protect files that require a huge amount of computational resources from being accidentally deleted.
ancient("..."): The timestamp of the input file is ignored and it’s always assumed to be older than any of the output files.
touch("..."): The output file should be “touched”, i.e. created or updated, when the rule has finished. Typically used as “flag files” to enforce some rule execution order without real file dependencies.
directory("..."): The output is a directory rather than a file.

Quick recap
In this section we’ve learned:

How to mark an output file as temporary for automatic removal.