Olamide Isreal 73e2eea4be Stop staging the 9.2 GB ChEMBL DB into every task workdir ...

GET_FINAL_METABOLITES_STATIC took chembl_db as a `path` input, so Nextflow
copied the ~9.2 GB SQLite DB into each task's work directory. With ~29
concurrent tasks that is hundreds of GB of I/O, against a process that also
declared only 1 GB of memory. Every task failed with exit 1 and retried ten
times, producing 746 errors and an empty 1b_final_metabolites/ output.

Pass the DB as a `val` path instead so tasks read it in place from the
dreamdock-data PVC, and give the process parameterised growing memory.

2026-07-28 10:05:17 +01:00

15 KiB

Executable File

Raw Blame History

View Raw