Can I get the list of actual commands that are used to run this pipeline?
I have been growing increasingly frustrated by this snakemake implementation. Some jobs are aborted with "non-zero" errors, but with empty error logs, sometimes it works using a local machine, but it doesn't work when using a cluster (which I need because of memory requirements), etc.
So far, my only "solution" is to completely remove the conda pore-c-snakemake environment after every single run, and hope that when I install the whole thing again, it would work.
I honestly think it would be more productive if I take my chances and assemble the commands myself. I am trying to parse those commands out from the snakemake rules, but it would be great if there was a location when the commands used in the pipeline were specified.
Thank you
Can I get the list of actual commands that are used to run this pipeline? I have been growing increasingly frustrated by this snakemake implementation. Some jobs are aborted with "non-zero" errors, but with empty error logs, sometimes it works using a local machine, but it doesn't work when using a cluster (which I need because of memory requirements), etc. So far, my only "solution" is to completely remove the conda pore-c-snakemake environment after every single run, and hope that when I install the whole thing again, it would work.
I honestly think it would be more productive if I take my chances and assemble the commands myself. I am trying to parse those commands out from the snakemake rules, but it would be great if there was a location when the commands used in the pipeline were specified. Thank you