sourmash integration - Githubissues

Arcadia-Science / metagenomics

A Nextflow workflow for QC, evaluation, and profiling of metagenomic samples using short- and long-read technologies

MIT License

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sourmash integration #5

Closed elizabethmcd closed 1 year ago

elizabethmcd commented 1 year ago

Description of feature

Add Nextflow modules for sourmash sketch, compare, gather, etc. for reads and assemblies

Sourmash sketch module updated with nf-core and PR approved

Integrate resulting sourmash files with Taylor's sourmashconsumr R package when ready for creating reports

taylorreiter commented 1 year ago

the nf-core taxprofile pipeline has been doing work on sourmash so lots of the modules we need are in the process of being updated or created:

sourmash sketch:
- PR: https://github.com/nf-core/modules/pull/2176
sourmash gather:
- PR: https://github.com/nf-core/modules/pull/2250
- issue: https://github.com/nf-core/modules/issues/2214
sourmash taxonomy:
- issue: https://github.com/nf-core/modules/issues/2261

vmikk commented 1 year ago

@taylorreiter Hello Taylor! sourmash tax annotate module was merged to nf-core yesterday. Could you please test it on your data? Also we are thinking to add sourmash summarize module, but I'm not sure how fast I'll do it.

taylorreiter commented 1 year ago

Thanks @vmikk! So excited to see this got merged! I plan to add it into the https://github.com/Arcadia-Science/seqqc pipeline first. I'll let you know how it goes over in that pipeline :)

elizabethmcd commented 1 year ago

addressed in #46 for sourmash infrastructure, issue #30 will include gather/taxonomy for db comparison and summaries