Pipeline Commands

DROP is Snakemake pipeline, so it is called with the snakemake command.

Dry run

Open a terminal in your project repository. Execute

snakemake --cores 1 -n

This will perform a dry-run, which means it will display all the steps (or rules) that need to be executed. To also display the reason why those rules need to be executed, run

snakemake --cores 1 -nr

Finally, a simplified dry-run can be achieved by executing

snakemake --cores 1 -nq

Calling snakemake --cores 1 without any additional parameters will execute the whole workflow. Snakemake requires you to designate the number of cores when running the snakemake command.

Parallelizing jobs

DROP’s steps are computationally heavy, therefore it is a good idea to run them in parallel. Snakemake automatically determines the steps that can be parallelized. The user simply needs to specify the maximum number of cores that Snakemake can take, e.g. for 10 cores:

snakemake --cores 10

Executing subworkflows

Every single module can be called independently.

snakemake <subworkflow>
Subworkflow Description
aberrantExpression Aberrant expression pipeline
aberrantSplicing Aberrant splicing pipeline
mae Monoalleic expression pipeline
rnaVariantCalling RNA Variant Calling pipeline

An example for calling the aberrant expression pipeline with 10 cores would be

snakemake aberrantExpression --cores 10

Rerunning the pipeline

When DROP is updated or jobs fail, the following commands can be used to rerun and troubleshoot.

Unlocking the pipeline

While running, Snakemake locks the directory. If, for a whatever reason, the pipeline was interrupted, the directory might be kept locked. Therefore, call

snakemake unlock

to unlock it. This will call snakemake’s unlock command for every module

Updating DROP

Every time a project is initialized, a temporary folder .drop will be created in the project folder. If a new version of drop is installed, the .drop folder has to be updated for each project that has been initialized using an older version. drop update will also reset the local project’s Scripts/ directory to match the installed version, so be sure to save any additional scripts or analyses in another location.

To do this run:

drop update

Skipping recomputation of files

If snakemake is interrupted and restarted, it will continue with the last unsuccessful job in the job graph. If a script is updated with minor change, e.g. when calling drop update, all jobs of the modified script and its downstream steps will be rerun. However, in some cases one might want to keep the intermediate files instead and continue with the missing files. In order to do so, first execute

snakemake <rule> --touch

for whichever rule or module you want to continue the computation. The --touch command touches all output files required by the pipeline that have already been computed. Omitting the rule will lead to accessing the complete pipeline. Afterwards, use

snakemake unlock

to unlock the submodules, so that the jobs that need to be computed can be identified.