Colton Baumler

A continuation using `awk` to parse a tab-separated dataset. ``` awk -F'\t' 'NR>1 && NF {print " - " $1}' assembly-test.tsv ``` Here I have called the awk program: -...

It would also be interesting to compare the accuracy of `sourmash gather` and `genome-grist` `MinSetCov` taxonomic outputs with and without `charcoal`.

I agree! They are completely different benchmarks. Mostly wanted to jot down the notion before it left me forever. Additionally, since we will be writing an analytical benchmark for computational...

There have been quite a few developments with sourmash's database scripts recently. @bluegenes and I will be meeting Wednesday to discuss where we stand currently with database creation/updating. I'll add...

Update! We have a bug that we are working through. #3191

Update: we also need to update the links in the issue https://github.com/sourmash-bio/sourmash/issues/3246 to the current database! Please hold! TL;DR - Two potential bugs with prefix and suffix of the idents....

The lineage file and databases for GTDB should now be in sync with this commit (https://github.com/sourmash-bio/database-releases/pull/6/commits/47cc39777d6fe838796f404cd3e5f0b078585869) I updated the scripts used to check the databases manifests for any updates as...

I have completed and (hopefully) address the bugs noticed above. The final draft of the 220 release from GTDB is located `/group/ctbrowngrp4/2024-ccbaumler-gtdb/gtdb-220` for the time being on the Farm. [A...

Sounds good. I also wrote this action for something else. It updates the `version:` section of the cff on release or publish. ``` # Inspired by https://github.com/FRBCesab/rcompendium/.github/workflows/update-citation-cff.yaml on: release: types:...

Sure, that is probably easier. There is also a test already set up to use the cff. Could add a line to assert version in: https://github.com/sourmash-bio/sourmash/blob/69edb6090fea99ea4a207e1829f1afbc2f8d6172/tests/test_sourmash.py#L42-L49 Using something like: https://github.com/sourmash-bio/sourmash/blob/69edb6090fea99ea4a207e1829f1afbc2f8d6172/doc/conf.py#L65-L71