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Hello Richard,
Thanks a lot for creating this automated pipeline.
I would like to try it with the aim of predicting neoantigen using solely RNAseq data.
As I understood from the paper and the doc…
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Hello,
Thank you for publishing your code. I am trying to use your workflow on a smaller dataset with a narrower temporal range than what you have in your preprint. I get the following error:
``…
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Hi again,
I have been getting the following error, and I haven found a solution. Among the things I tried is running the command with the -ignore-incomplete flag, to no avail.
The error is the …
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kgwasflow/lib/python3.11/site-packages/kgwasflow-1.2.3-py3.11.egg/workflow/rules/common.smk, line 91:
sequence item 0: expected str instance, PosixPath found
Line 91 is :
config_file= ", ".join(w…
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**Describe the bug**
Mamba not detected in snakemake when hybracter is run on the cluster via slurm. hybracterENV installed with miniforge3.
**To Reproduce**
1. conda activate hybracterENV in …
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showyourwork version: 0.4.4.dev37+g1526059 (latest on main branch as of August 1)
snakemake version: 7.15.2
Python version: 3.9.19
Minimal reproducible example:
In one of my projects I changed…
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Hello,
I am following the helpful tutorial for running the pipeline using demo data on my local machine (Intel iMac). Unfortunately, I am running into a roadblock. Everything seems to install fine …
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https://github.com/NBISweden/GenErode/blob/main/workflow/rules/9_merge_vcfs.smk#L266C23-L266C42
This command does not remove sites that are coded as heterozygous sites but are fixed derived sites (…
verku updated
3 months ago
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Hello everyone,
I've tried using the config.16s.yaml with the test data it works fine. However, when I try running a dry run using my own data it prompts me this error.
You will not be able to…
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Hi,
When I run `sq.gr.nhood_enrichment(sdata["table"], n_jobs=10, cluster_key='id')`, the following error occurred:
```
No matching definition for argument type(s) readonly array(uint32, 1d, C), ar…