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My current best and quickest solution for retrieval of repeat annotations is to make the RepeatMasker download link configurable via the `config.yaml`. However, this has several restrictions:
1. It…
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now that we provide our own (non-snakemake) entry point, charcoal itself needs to be installed in order to run stuff.
in the short term, I think we can use the pip install magic provided by conda t…
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Following up on Issue #1, now that there is a Snakemake based workflow for the RECAST hello world example, we should additionally add a workflow and instructions to be able to run this workflow on REA…
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Go through all `README` and other documentation files and check for missing/broken links, unclear explanations etc. Either fix yourself or reach out on Slack to clarify how to fix. Create new issues t…
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**Snakemake version**
```
$ snakemake --version
7.19.1
```
and I checked against the changelog, apparently nothing related has been worked on since 7.19.1.
**Describe the bug**
When m…
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Hi,
I am trying to use tibanna to launch snakemake workflows on AWS. However, I am constantly running into an error (as I can see on the cloud watch)
`{
"error": "ClientError",
"cause": {
…
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https://nextstrain.org/docs/bioinformatics/customizing-a-build
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[Episode 7 (Resources and Parallelism)](https://carpentries-incubator.github.io/workflows-snakemake/07-resources/index.html) provides a good opportunity to introduce [temporary files in Snakemake.](ht…
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I recently spent a lot of time chasing down a bug in one of my Snakemake workflows, which ended up being the result of a typo: the key used in the Snakefile didn't match the key in the config file, in…