Lucas Czech

Hi @meixilin, as you originally posted this in #36, I assume you are also using the `restrict-regions` option? If so, then combining this with the contig grouping option (`contig-group-size !=...

Hi @meixilin, just had another look at this, and indeed it seems to be a known issue with Snakemake that I brought up with the developers already (https://github.com/snakemake/snakemake/issues/2980), but with...

Hi Luca, > I am running Grenepipe on a 164-thread cluster computer with 3 TB of RAM. > My dataset consists of 306 samples. Initially, I thought it would be...

Hi Luca, thanks for the details! At first glance, it is not obvious to me what's wrong there - let's see what we can find out. ## Deleting on different...

Hey Luca, Very interesting case. Thanks for the new tests! What do you mean by that: > As before, the deleted BAM files were only those in the pipeline's default...

Hm, now I am even more confused :-D I hope it's okay to be pedantic here - the devil is often in the details with such things! > I ran...

Ah accidentally uses some keyboard shortcut that closed the issue... sorry for that. Open again now!

Ah I see. And the bam files that you copied into `mapping/final/` are the ones being deleted? Yeah that is the issue then: You are putting the files into the...

Hi Luca, thanks for the report, and I am happy to hear that this solves your issue! Yeah, this is indeed a confusing combination of circumstances leading to the issue....

Hey Rifa, thanks for reporting this! Yes, I can see how this is happening... bcftools in the rule tries indeed to read form the `done` file, which it shouldn't. Seems...