FAQs

How many capsules or datasets can be added to a pipeline?

As many as you need.

Where are files in the Results Bucket stored?

In an S3 bucket.

Are intermediate pipeline results (results passed between capsules) saved after a Reproducible Run?

After a Reproducible Run, only outputs from capsules connected to the Results Bucket will be saved in Code Ocean. However, intermediate results will be saved to an S3 bucket. These files are automatically deleted after 30 days so as to not take up unnecessary storage.

Can a capsule that uses absolute paths be used in a pipeline?

From within a capsule’s code directory, absolute paths (e.g. /root/capsule/results/) and relative paths (e.g. ../results) can be used to reference other folders. In a pipeline, Nextflow will clone the capsule/ folder of each capsule which will cause the pipeline to crash if absolute paths were used.

Best practice: always use relative paths in a capsule so that they can be easily used in a pipeline

Are GPUs supported in pipelines?

Not yet but this feature is coming.

In a pipeline, do my capsules use the same resources that I configure in the capsule environment editor?

Since pipelines run on AWS batch, the capsule’s compute resources will be ignored and by default the capsule will be allocated 1 core and 8GB of RAM. Customize these resources by double clicking on a capsule in the Visual Pipeline Editor to open the capsule settings. Then set the desired CPU (max 192 cores) and memory (max 4096GB).