HealthOmics tries to provide a consistent implementation of call caching across workflow engines. There are some differences based on how each workflow engine handles specific cases:
-
Nextflow
-
You can turn off caching for individual tasks by using the cache false directive. For information about this directive, see the Processes
in the Nextflow specification. -
HealthOmics uses Nextflow lenient mode, but doesn't support deep caching mode.
-
Caching evaluates each individual S3 object if you use a glob pattern in the S3 path to the inputs for a task. If you add a new object, HealthOmics recomputes only the tasks that use the new object.
-
HealthOmics doesn't cache task retries. This behavior is consistent with Nextflow’s default behavior.
-
-
WDL
-
HealthOmics supports the new “directory” type for inputs when you use the development version of the WDL workflow. For call caching, if any object in the directory changes, HealthOmics recomputes all tasks that input the directory.
-
HealthOmics supports task-level caching, but not workflow-level caching.
-
-
CWL
-
Constant outputs from tasks aren't explicitly visible from the manifests. HealthOmics caches constant outputs as intermediate files.
-
