My question is regarding recovering/obtaining commands of individual tools after a successful pipeline run. Unfortunately, the pipeline run was not executed with the required option --snakemakeOptions="-p". This would be relevant for me because the pipeline has run successfully and the results are generated. I would want to avoid re-running it because of obvious compute times.

One possible alternative would be to use --snakemakeOptions="-np" and generate a dry-run based command executions. This may not be the same thing as some of the command-line arguments of certain tools are "greped"/"awked"/"seded" (excuse my made up verbs) and the real arguments will not be printed in the log file.

I imagine the most appropriate thing for me was to check this prior to running it but I didn't :(

Any help would be greatly appreciated and if I may suggest enabling this option (--snakemakeOptions="-p") by default in the snakePipes and let people choose to disable should they wish by a flag during execution. If any member of the snakePipes team think it is relevant, I can link this up as an enhancement issue on the github page.

Best,

Kashyap