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nextflow clean

Clean up cache and work directories.

Usage​

$ nextflow clean [run_name|session_id] [options]

Description​

When you run nextflow in a directory, it creates a project-specific .nextflow.log file, a .nextflow cache directory, and a work directory. The clean command removes these files from previous runs. Run nextflow log -q to list the available run names and session IDs.

If you do not provide a run name or session ID, clean removes the files for the latest run.

Options​

-after​

Clean up runs executed after the specified one.

-before​

Clean up runs executed before the specified one.

-but​

Clean up all runs except the specified one.

-n, -dry-run​

Print names of files to be removed without deleting them.

-f, -force​

Force the clean operation.

-h, -help​

Print the command usage.

-k, -keep-logs​

Remove only temporary files, retaining execution log entries and metadata.

-q, -quiet​

Do not print names of files removed.

Examples​

Dry run to remove work directories for the run name boring_euler:

$ nextflow clean boring_euler -n

Would remove work/92/c1a9cd9a96e0531d81ca69f5dc3bb7
Would remove work/3f/70944c7a549b6221e1ccc7b4b21b62
Would remove work/0e/2ebdba85f76f6068b21a1bcbf10cab

Remove work directories for the run name boring_euler:

$ nextflow clean boring_euler -f

Removed work/92/c1a9cd9a96e0531d81ca69f5dc3bb7
Removed work/3f/70944c7a549b6221e1ccc7b4b21b62
Removed work/0e/2ebdba85f76f6068b21a1bcbf10cab

Remove the execution entries except for a specific execution:

$ nextflow clean -but tiny_leavitt -f

Removed work/1f/f1ea9158fb23b53d5083953121d6b6
Removed work/bf/334115deec60929dc18edf0010032a
Removed work/a3/06521d75da296d4dd7f4f8caaddad8

Dry run to remove the execution data before a specific execution:

$ nextflow clean -before tiny_leavitt -n

Would remove work/5d/ad76f7b7ab3500cf616814ef644b61
Would remove work/c4/69a82b080a477612ba8d8e4c27b579
Would remove work/be/a4fa2aa38f76fd324958c81c2e4603
Would remove work/54/39116773891c47a91e3c1733aad4de

Dry run to remove the execution data after a specific execution:

$ nextflow clean -after focused_payne -n

Would remove work/1f/f1ea9158fb23b53d5083953121d6b6
Would remove work/bf/334115deec60929dc18edf0010032a
Would remove work/a3/06521d75da296d4dd7f4f8caaddad8

Dry run to remove the temporary execution data for a specific execution, while keeping the log files:

$ nextflow clean -keep-logs tiny_leavitt -n

Would remove temp files from work/1f/f1ea9158fb23b53d5083953121d6b6
Would remove temp files from work/bf/334115deec60929dc18edf0010032a
Would remove temp files from work/a3/06521d75da296d4dd7f4f8caaddad8
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