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Hello, I'm a graduated student studying bioinformatics in South Korea.
I'm trying to do detect extrachromosomal DNA (ecDNA) in nanopore long-read targeted sequencing data.
I followed the workflow …
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Hi,
When I executed the command "snakemake --cores all --software-deployment-method conda", the following error occurred:
```shell
$ snakemake --cores all --software-deployment-method conda
Assumi…
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To create initial `snakemake` workflow for `ANIb` method, we need to do the following:
1. Update the Makefiles to include the installation of `blast`.
2. Write Initial Workflow to Generate Appro…
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Work coming from the BGE hackathon in Leiden. Reporting of products made should go in the report here: https://docs.google.com/document/d/1if6ukMKN3xHQHAwGEQPhhgvp7iQcFnauj4W1ZtIs8wk/edit
Aim is to w…
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Hi, snakemake team!
I want to use argparse module set a custom parser to pass the argument of snakemake, then run the snakemake. I noticed that a module spacemake did it by snakemake.snakemake() at t…
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I'm trying to update my snakemake workflow to v8+
My nuisance so far is the following. I submit my workflows as a job in the login node from where snakemake with the executor do their thing. Proble…
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### Lesson Title
Snakemake for Bioinformatics
### Lesson Repository URL
https://github.com/carpentries-incubator/snakemake-novice-bioinformatics
### Lesson Website URL
https://carpentries-incubat…
gperu updated
1 month ago
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**Snakemake version**
Important: the bug _only_ manifests with Python 3.11 (3.11.9 at time of testing). It does _not_ manifest with Python 3.12
Confirmed issue is reproducible with:
- snakemake…
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**Snakemake version**
8.4.2
**Describe the bug**
As of PR #1407 fixing issue #1398, `SNAKEMAKE_PROFILE` cannot be passed to cluster jobs. We frequently used this as a required env varia…
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from @cmeesters:
> we recommend using Snakemake wrapper to handle awkward programs to increase the stability of workflows
> wherever possible. There is not even an outlook to wrappers. This is - I…