Cache Behavior

adagio run requires a cache directory:

adagio run --pipeline pipeline.adg --cache-dir /path/to/cache

That directory is a shared QIIME cache, not a general scratch folder.

What the cache is for

Adagio uses the cache to reuse previously completed task results when:

When that happens, Adagio can replay the cached result instead of rerunning the task.

Reuse happens at the task level, not only at the whole-pipeline level.

That means:

change one downstream parameter and upstream unchanged tasks can still be reused
change an early input or parameter and all dependent downstream tasks will rerun

Normal behavior:

adagio run --pipeline pipeline.adg --cache-dir ./cache

Disable reuse for one run:

adagio run --pipeline pipeline.adg --cache-dir ./cache --no-reuse

--no-reuse keeps the run from loading matching prior results from the selected cache.

Pick one stable directory and keep using it for related runs.

Examples:

This is usually better than creating a new cache path for every run, because reuse only helps when later runs can see earlier results.

Do not confuse these:

Removing output files does not clear the cache. Clearing the cache does not remove previously copied final outputs.

Use the dedicated command:

adagio cache clear --cache-dir /path/to/cache

This command checks that the target really looks like a QIIME cache before deleting it.

The cache works across both Docker and Apptainer execution as long as the run points at the same cache directory.

Runtime config changes do not disable caching by themselves. What matters is whether the resolved task invocation is the same.

Use --no-reuse when you want to: