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## Context
In a pathogen repo, there will technically be 3 separate workflows that can be run: ingest, phylogenetic, and nextclade.
It's unclear how we want to set up the standardized GitHub Actio…
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Aim to follow Best Practice recommendations
- [ ] Restructure repo layout as per https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#distribution-and-reproducibility
- [ ] Utilis…
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This issue is to kick off a discussion of strategy around documentation content, with an eye toward issue #43, implementing documentation of workflows in sphinx.
There are a number of different ver…
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Wednesday August 25 from 9 am - 11:30 PDT
Instructors: Abhijna Parigi and Titus Brown
Moderator: Marisa
Helpers:
Zoom link:
Description:
>This two hour workshop will introduce attendees…
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**Describe the bug**
In snakemake (v8.4.7), "--cluster-status" is not supported, and thus the "cluster-status" in [config.yaml](https://github.com/gbouras13/hybracter/blob/9250ad5a0ed91b04d7976503db8…
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Good point you brought up in the PR. Three thoughts:
1. Good idea to keep Snakemake in the title because it's specific
2. I still would like to add Python as it adds generality and discoverability…
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# [Snakemake Monitoring](https://snakemake.readthedocs.io/en/stable/executing/monitoring.html)
Snakemake supports [`panoptes`](https://github.com/panoptes-organization/panoptes) a server (under devel…
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Hello,
the workflow ran almost through to the end. But the following Error occurred:
Error in rule diffexp_datavzrd:
jobid: 41
input: results/datavzrd/diffexp/model_X.yaml, results/ta…
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**Is your feature request related to a problem? Please describe.**
I often implemented ETL workflows where some step depends or produces on a table or view in a relational database. In many cases, yo…
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### Context
Originally proposed in https://github.com/nextstrain/cli/issues/373#issuecomment-2174603786
It'd be helpful to have a summary of workflow stats in the form of a [Snakemake report](ht…