Start project with readme, environment, and itial snakemake workflow to execute sourmash commands #1
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taylorreiter
changed the title
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and maybe of interest to @mertcelebi...this is a demo of how I'm expecting code pushes and PRs to look for data analysis projects. |
| ## Download sourmash databases & taxonomy files | ||
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| rule download_genbank_bacteria_zip_k21: |
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I'm assuming this will change to pulling from S3 once we have the databases bucket figured out
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yes! or be an ifelse/parameterized statement to avoid download. Although...download ended up being less horrible than I thought...I was using some weird links originally and it was taking FOREVER to get the data, but then I updated to these and it was 50mb/s and that was perfectly acceptable. See sourmash-bio/sourmash#2179 and sourmash-bio/sourmash#2136
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Awesome, thanks @elizabethmcd! |
| import argparse | ||
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| def main(): | ||
| p = argparse.ArgumentParser() |
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Might wanna check click for creating command-line runnable scripts! It's slightly neater than argparse IMO. Or you can try to use the help option for add_argument in argparse to clean up the comments.
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for @taylorreiter - we use click in many places - e.g. genome-grist link. I prefer argparse for complex situations (b/c it's been around longer, has more stackoverflow answers for oddball things) but click is way friendlier!
| - defaults | ||
| dependencies: | ||
| - sourmash-minimal=4.4.3 | ||
| - pandas |
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we should probably pin versions of all of these (like you did in environment.yml)
| shell:''' | ||
| python scripts/sig_to_csv.py {wildcards.ksize} {input} {output} | ||
| ''' | ||
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nit: this is more of an aesthetic thing, but I like the consistency of it. Using a linter (or a text editor plugin), we should make sure there is only a single trailing newline at EOF
This PR is the first PR for this repository. It does two things:
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Snakefile: snakemake workflow that coordinates the execution of sourmash commands on metagenome assemblies. I have run this workflow and can confirm it runs correctly :) Eventually, I will add notebooks that will visualize the output of the workflow, but I wanted to have this portion reviewed before dumping a bunch more code.b.
environment.yml: specifies the run environment for the workflow. SeeREADME.mdfor more information.c.
envs/*yml: environments created and managed by the snakefile (see theconda:directive in each rule to know which environment is used by each step of the workflow.d.
scripts/: folder for auxiliary scripts executed by the snakemake workflow. In this case, it only includessig_to_csv.py, a python script to convert a sourmash sketch into a csv file.e.
inputs/metadata.csv: metadata file encoding sample names. Used by the snakefile to determine file prefixes.