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Our pipeline requires that users install every variant caller at runtime, even if they don't actually use some of them.
For example, DELLY is not used by the pipeline by default, but it is still inst…
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### Problem Description
Currently, rotary gives every multithreaded rule the complete set of CPU threads. However, these jobs often only sometimes use all these available threads all the time. For …
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Hi @metaGmetapop! The pipeline fails during the Fst calculation step. I get the following error message
> Error in eval(jsub, SDenv, parent.frame()) : object 'V1' not found
> Calls: [ -> [.data.ta…
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Hi Nick,
I am still having trouble updating my database with custom MAGs. I run snakemake using the following command and config file:
[config-update.yaml.txt](https://github.com/leylabmpi/Struo2/…
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**Snakemake version**
7.19.1
**Describe the bug**
Snakemake linter behavior changed on run directives compare to version 7.12.0
**Logs**
```bash
(mosaicatcher_env) [tweber@se…
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I was working on fixing conda environment support for windows.
In the process I stumbled on a bug in "jupyter notebook" tests.
I get a validation error from the temporary notebooks where snak…
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Building DAG of jobs...
Error: Directory cannot be locked. Please make sure that no other Snakemake process is trying to create the same files in the following directory:
/home/ZZZ_Macc/tools/EukDet…
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I try to install snakemake from conda-forge on a fresh conda environment with python 3.7 (or 3.8 or 3.9), but while other packages install fine, snakemake responds with:
>
> Could not solve for e…
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Hi,
I'm trying to run McClintock for a large number of isolates. I submitted the first batch of 20 and they all failed with the same error message with malformed bed entries:
```
PROCESSING …
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Hi @aineniamh,
I was wondering if you have any information on the resources we should give Piranha to maximize its efficiency along with if you've tried to make use of snakemake's profiles feature …