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Or other tools, NextFlow?
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Follow up to https://github.com/nextstrain/ncov-ingest/pull/451.
We are using the Snakemake `--stats` flag to get workflow stats for [GISAID](https://github.com/nextstrain/ncov-ingest/blob/f5f238b…
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From review by @cmeesters:
*Chapter 11 - Designing a new workflow*
This Chapter needs a major revision:
* the assembly part comes out of the blue and is unrelated to everything before. If you w…
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**Is your feature request related to a problem? Please describe.**
Snakemake's [module](https://snakemake.readthedocs.io/en/stable/snakefiles/modularization.html#modules) functionality is incredibly …
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Make accessible methods defined in the *.smk files. On runtime everything will be merged to the same file
E.g.
```
# rules/common.smk
def foo():
pass
# rules/foo.smk
a = foo() #
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**Is your feature request related to a problem? Please describe.**
no problem per se, just a tool that *could* know all the variables needed for calculation
**Describe the solution you'd like**
…
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I was playing around with genomepy and accidentally wiped my config.yaml clean. This gave me the error that sys was not defined:
```
Traceback (most recent call last):
File "/home/sande/Desktop/s…
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Don't know how easy this is to do with an extension, but an annoyance of writing workflows in VS Code is the implicitly defined `snakemake` global variable. The type checker is not aware of this and w…
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REANA allows to preview some files directly from the web UI.
In particular, reana-workflow-controller can set the following content types when returning the contents of a file:
https://github.com/…
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I discussed barriers to running SPRAS in a high-throughput computing environment with @bbockelm and @jhiemstrawisc. One challenge is that each algorithm's run function executes some Python code to set…