Output Settings#

Working Directory - [path]: Directory where CPAC should store temporary and intermediate files. Path should not contain spaces.
Output Directory - [path]: Directory where CPAC should place processed data. This can also be an S3 bucket path prepended with ‘s3://’. Path should not contain spaces.
Log Directory - [path]: Directory where CPAC should place run logs. Path should not contain spaces.
Crash Log Directory - [path]: Directory where CPAC should write crash logs. Path should not contain spaces.
AWS Output Bucket Credentials (optional) - [path]: If setting the Output Directory to an S3 bucket, insert the path to your AWS credentials file here.,
S3 Encryption - [On, Off]: Enable server-side 256-AES encryption on data to the S3 bucket,
Write Extra Functional Outputs - [On, Off]: Include extra versions and intermediate steps of functional preprocessing in the output directory.
Write Debugging Outputs - [On, Off]: Include extra outputs in the output directory that may be of interest when more information about intermediate steps is needed.
Enable logging - [On, Off]: Whether to write log details of the pipeline. run to the logging files..
Remove Working Directory [On, Off]: Deletes the contents of the Working Directory after running. This saves disk space, but any additional preprocessing or analysis will have to be completely re-run.)
Create organized output directory - [On, Off]: Create a simplified version of the output directory.
Regenerate Outputs - [On, Off]: Uses the contents of the working directory to regenerate all outputs and their symbolic links. Requires an intact working directory from a previous C-PAC run.
Enable Quality Control Interface - [On, Off]: Generate quality control pages containing preprocessing and derivative outputs.

Configuration Without the GUI#

The following nested key/value pairs will be set to these defaults if not defined in your pipeline configuration YAML.