DROP is Snakemake pipeline, so it is called with the
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
snakemake --cores 1 without any additional parameters will execute the whole workflow. Snakemake requires you to designate the number of cores when running the
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
Every single module can be called independently.
||Aberrant expression pipeline|
||Aberrant splicing pipeline|
||Monoalleic expression pipeline|
||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
to unlock it. This will call snakemake’s
unlock command for every module
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:
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
to unlock the submodules, so that the jobs that need to be computed can be identified.