Tessa Pierce Ward

[WIP] add rules for protein mapping

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This PR introduces rules to allow mapping nucleotide reads to protein references using Paladin. not functional yet. Main questions at this point: - Do we want to just do this...

https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html?highlight=temp#standard-resources As of `v6.5`, snakemake supports `tmpdir` within the `resources` directive: > ### Standard Resources > There are three standard resources, for total memory, disk usage and the temporary directory...

Brought on by thinking about fastp (I/O bound) -- would be great to use `base_tempdir` to write temp files for any process like this. We can use `temp()` as in...

In thumper, I'm doing genome and contig gathers --> LCA at the same time, to avoid building LCA twice. Figured I'd port my changes back over here, in case they're...

Currently, if a genome is present in the lineages file, but not in the genomes txt file, you get the following error. ``` charcoal run newproject.conf -n ** WARNING: lineage...

current output is not super user-friendly :) ``` charcoal run orthodb.conf -n Traceback (most recent call last): File "/home/ntpierce/miniconda3/envs/charcoal/lib/python3.8/site-packages/snakemake/io.py", line 1372, in _load_configfile with open(configpath) as f: FileNotFoundError: [Errno 2]...

`calculate` error when using `-p blastp`

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Thanks for your help with the previous issue - I'm back with a different one! I'd like to use `blastp` for some AAI calculations. I used `conda` to install `blastp`...

`sourmash` submission

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**Submitting Author:** Tessa Pierce-Ward (@bluegenes) **All current maintainers:** @ctb, @luizirber, @bluegenes **Package Name:** sourmash **One-Line Description of Package:** `sourmash` is a command line tool and Python library for sketching collections...

[note: this is an experimental/draft PR and should not be merged as-is] ref #72 In sourmash taxonomy, we're adding utils to use the `LIN` taxonomic framework, which allows for greater...

In sourmash taxonomy, we're adding utils to use the `LIN` taxonomic framework, which allows for greater flexibility and specificity compared with standard taxonomic ranks. For example, if only certain strains...