Frequently asked questions (FAQ)

StaG-mwc is designed to be fairly flexible. This section answers common questions on how to best utilize StaG-mwc’s flexibility. Please help expand this section by making a Pull Request with suggestions.

Skip read QC

In some cases your data has already been subjected to adapter and quality trimming so you want to skip that step. In StaG-mwc it is possible to bypass both the read QC step and the host removal steps if you need to. In order to do so, we must “trick” Snakemake into thinking that those rules have already been performed. The rules for read QC and host removal are configured with bypasses so that if the user sets host_removal: False or qc_reads: False, those steps will be bypassed by creating symlinks directly to the input files in the respective output directories.

Skip host removal

It is possible to skip host removal. This might be appropriate for example when processing environmental samples that do not need host removal. It is implemented in StaG-mwc in a special way: if the user sets host_removal: False in the configuration file then StaG-mwc will put symlinks to the qc_reads output files in the host_removal output directory. This “tricks” Snakemake into thinking that host removal actually occured, enabling it to complete the dependency graph to process the data in downstream steps.

Pipeline stopped unexpectedly

If pipeline ends with error or if the session is locked after being unexpectedly disconnected and the pipeline needs to be restarted, you can try to remove slurm metadadata files before restarting pipeline using:

(base)$ rm -rfv .snakemake/metadata