omegatro
commented
1 year ago Partially this is solved by using mv or cp -p to preserve timestamps on output files. Some files, however, still trigger full reprocessing with reason: Forced excecution for quality control rule and "File updated by another job". Further check required.
Currently when combining the pipeline outputs from different runs, the snakemake will reprocess part of the input samples even if the outputs exist.
Potential lead: if files were copied, the timestamps are updated leading to "Updated input files" trigger