potential command lines

[ctb]

I'm thinking of doing the command line for this snakemake app differently; right now I'm not using config files much, just the sample name. How does the below sound?

each command would be successive & snakemake-ified, of course, so you could run the last one and it would do all the previous ones.

# download SRA metagenome
genome-grist download-sra HSMA33MX

# trim and abundtrim SRA metagenome
genome-grist trim-reads HSMA33MX

# make a sourmash signature
genome-grist smash HSMA33MX

# download, abundtrim, genbank gather SRA metagenome
genome-grist gather HSMA33MX

# download genbank genomes based on gather results
genome-grist download-genomes HSMA33MX

# do iterative read mapping etc based on gather
genome-grist map HSMA33MX

# summarize content, abundance, taxonomy, mapping based on gather => pretty graphs etc.
genome-grist summarize HSMA33MX

# extract spacegraphcats neighborhoods
genome-grist neighborhoods HSMA33MX

[ctb]

(this is rapidly taking on some of the "hey we need generic workflows for sourmash" needs 😆 )

[ctb]

but, anyway, part of the point is that we can reimplement and optimize some of these steps underneath, based on expanding capabilities of sourmash/etc.

[luizirber]

(this is rapidly taking on some of the "hey we need generic workflows for sourmash" needs laughing ) but, anyway, part of the point is that we can reimplement and optimize some of these steps underneath, based on expanding capabilities of sourmash/etc.

so sourmash becomes a more focused "power tool", and other tools/pipelines can explore and extend before it crystalizes back into sourmash? I think this is good to avoid feature-creep in sourmash, as well as maintaining sourmash liable to its API/semantic versioning changes (because more tools will be depending on it).

(just to be clear, this is kind of what I already think about the Rust/Python parts of sourmash =])

[ctb]

eet eez abstractionz all ze vey down