I made some small time/resources edits that ignoreable. The two I want to draw your attention to are in sv.smk and itervals.smk
I made changes to the smoove relevant rules because 1) the -x removes INFO fields that are needed to merge smoove vcfs together for future genotyping/population vcfs. 2) The -d calls mosdepth to make depth measurements that aren't really needed, I might've gotten an error once and deleted the option. I removed the filter step, again it makes the vcf not helpful for merging / population level genotyping. I rewrote it to be a default smoove call and rename outputs with wags convention. 3) changed the sv.done to recognize the new smoove output.
The other small but maybe relevant change I made was in intervals.smk: scatter_intervals. Whatever the default time and resources parameters are (I think out of memory was the error that inspired the change), it wasn't enough and I kept getting failures.
I made some small time/resources edits that ignoreable. The two I want to draw your attention to are in sv.smk and itervals.smk
I made changes to the smoove relevant rules because 1) the -x removes INFO fields that are needed to merge smoove vcfs together for future genotyping/population vcfs. 2) The -d calls mosdepth to make depth measurements that aren't really needed, I might've gotten an error once and deleted the option. I removed the filter step, again it makes the vcf not helpful for merging / population level genotyping. I rewrote it to be a default smoove call and rename outputs with wags convention. 3) changed the sv.done to recognize the new smoove output.
The other small but maybe relevant change I made was in intervals.smk: scatter_intervals. Whatever the default time and resources parameters are (I think out of memory was the error that inspired the change), it wasn't enough and I kept getting failures.