Frequently Asked Questions

General Questions

What is the purpose of this pipeline?

Causeway was built to perform Mendelian Randomization and sensitivity analysis for a large number of exposure-outcome phenotype combinations.

Who is the intended audience for this pipeline?

The intended audience of this pipeline are bioinformaticians and Epidemiologists/Geneticists familiarized with command-line tools.

What input data formats does the pipeline accept?

It accepts only summary statistics in GCTA-Cojo format. For more info about inputs, check the usage input section.

What are the key outputs of the pipeline?

The key output is a report with the main analysis findings. You can check more about this and the other outputs at the outputs section.

Installation and Setup

What are the minimum system requirements to run the pipeline?

You will need a system with a minimum of 4 cores, 8GB RAM, 20GB of storage and Linux, MacOS or Windows Subsystem for Linux (WSL) with Nextflow and a container manager installed. More information this can be found at the system requirements section.

Do I need to install any specific software or dependencies before running the pipeline?

Apart from Nextflow and a container manager, you won't need to install any dependencies.

How do I install and configure the pipeline on my system?

You can download, install and set the pipeline with a single command:

nextflow pull juliaapolonio/Causeway

Usage

How do I execute the pipeline with example input data?

To execute the pipeline with minimal test data, you will need this command:

nextflow run juliaapolonio/Causeway -profile test,YOURPROFILE --outdir <OUTDIR>

Where YOURPROFILE will be the container executor you have in your machine.

What command-line options are available for customizing the pipeline?

A list of optional flags can be found in the optional flags section.

How do I specify a custom configuration file?

You can add your own configuration file as a profile in the conf directory. Alternatively, you can check if there is an existing configuration profile for your institution at nf-core/configs documentation.

Can the pipeline be run on a cluster or cloud environment?

Yes, Nextflow can handle lots of cluster and cloud computing environments, such as Slurm, Google Cloud, AWS. More information about it can be found at Nextflow executor documentation.

What should I do if my pipeline run is interrupted?

You can run it again with the same parameters and adding the -resume option, which will search for the execution cache.

Troubleshooting

What should I check if the pipeline fails with an error?

Where can I find detailed logs of the pipeline execution?

For logs of the whole pipeline execution, you can check the pipeline_info folder on the output directory. If you want a log of specific task, you can check its hash in the work directory. See Nextflow documentation on execution reports for more details.

Why is the pipeline taking longer than expected to execute?

This pipeline should take a while to finish if using large data (e.g. the application analysis took 58 hours using 50GB of RAM in a cluster). If it is abnormally longing to finish, you can check the input data of the tasks that are running.

What does it mean if some outputs are missing from the results directory?

It probably means that a silent error happened. You can check the log files from the task to see if anything went wrong with the execution.

How can I debug issues with specific modules (e.g., rendering reports, statistical analyses)?

For each task, Nextflow has a hash that can be found in the work directory. Inside the task folder, you can check the .command.log or .command.err to see if there's anything unusual.

Results and Outputs

What do the output files in each directory mean and how do I interpret the metrics and visualizations produced by the pipeline?

A comprehensive description of the outputs and its interpretations can be found at the outputs section.

What should I do if I suspect a bug in the output files?

This tool is still under testing and bugs can happen. If you feel that something went wrong with the analysis, please leave an issue with a reproductible example.

Can I customize the report generated by the pipeline?

You can edit the report by directly editing the report module script.

Customization

Can I add new analysis modules to the pipeline?

Yes! Since the pipeline is all built based on modules, you can add your own analysis and integrate with the pipeline at main.nf, or use this pipeline as a subworkflow.

How do I use my own scripts or tools within the pipeline?

You will have to build a module and integrate it to the main workflow.

Is it possible to change the default parameter values?

Not yet. Only by editing the source code for now.

How can I incorporate additional datasets into the analysis?

You can use any exposure/outcome/reference you want, it just need to follow the usage input guidelines.

Performance and Optimization

What steps can I take to optimize pipeline performance?

Nextflow already does that to you! But if you feel that you need something more custom, you can change nextflow.config or conf/modules.config files.

Can I run specific modules independently?

Yes, you can use Causeway modules to build your own workflow.

Support and Contributions

Where can I report bugs or request new features?

You can do these requests by raising an issue.

Is there a user community or forum for pipeline-related discussions?

For Nextflow users, there's the nf-core community! For this specific pipeline, there's no discussion forum.

How can I contribute to the development of the pipeline?

If you want to make an improvement in the code, you can open a Pull Request at the Causeway's repository. If you want to be a continuous collaborator, please reach one of the authors.

Is there a citation for this pipeline?

The paper is in reviewing process but you can cite our BioarXiv preprint:

Can I use the pipeline for commercial purposes?

Yes, Causeway's license allows the use for commercial purposes.