C. Titus Brown
C. Titus Brown
it's good to note that grist is built around snakemake, and will accept all snakemake options. should suggest using `-k` as default, too, to keep going past errors.
after https://github.com/dib-lab/genome-grist/pull/199, khmer will only be required for the k-mer counting step that is part of reporting. there are other, supported k-mer counting software packages :)
and maybe `sigs/` to `sourmash-sigs/` or something. reasoning: `gather` is internal jargon used in sourmash, and it's probably better to make it clear that it's all sourmash output.
right now it's under `genome_grist/conf/` but I think I like it better under `genome_grist/`. We could also move `genome_grist/conf/env` to just `genome_grist/env/`
In v0.9.0, there are a number of changes to take into account if you are already working with genome-grist. If you want to take advantage of these new features without...
Sometimes when running grist I get an error like this: ``` gzip: outputs.private/genomes/.genomes.podar: unexpected end of file [Mon Sep 26 07:42:47 2022] Error in rule samtools_mpileup_wc: ``` and I can't...
if I hit ctrl-c while running genome-grist, frequently it kills off snakemake and I need to run an `--unlock`, which the genome-grist command line does not make easy. two independent...
might be nice to assemble the downloaded and trimmed metagenomes.
off the top of my head, * the prefetch + gather steps can now be done in a single rule, because we can now output the prefetch CSV at the...