KRAKENUNIQ_BUILD is deleting the symlinked inputs when keep_intermediates is false.

[mahesh-panchal]

Have you checked the docs?

• nf-core website: troubleshooting
• nf-core modules documentation

Description of the bug

KRAKENUNIQ_BUILD has the following code

    custom_db = custom_library_dir ? "mkdir ${prefix} && mv library taxonomy ${custom_seqid2taxid} ${prefix}" : ""
    run_cleanup = keep_intermediate ? "" : "find -L ${prefix} -type f -not -name \"*.kdb\" -type f -not -name \"*idx\" -not -name \"taxDB\" -not -name \"*.counts\" -delete"

The input folders are moved to the prefix folder, and then files within them are deleted which is deleting my input files.

Command used and terminal output

Relevant files

No response

System information

No response

[mahesh-panchal]

@jfy133 This affects taxprofiler too most likely.