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If I go here:
https://www.katacoda.com/johanneskoester/scenarios/snakemake-intro
following the link given here:
https://www.youtube.com/watch?v=hPrXcUUp70Y
I see the following error:
```
$ d…
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The following command line fails on franklin:
```
cd /mnt/stripe/shpynov/chipseq-smk-pipeline
source activate snakemake
snakemake all --use-conda --cores 28 --config work_dir=/mnt/stripe/bio/raw-…
olegs updated
5 years ago
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**Snakemake version**
6.7.0
**Describe the bug**
Both `SynchronousClusterExecutor` and `GenericClusterExecutor` are initialized with the `cores` parameter set to `None`
https://github.co…
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**Snakemake version**
6.6.1
**Describe the bug**
I've been running into issues when I try to run `snakemake --generate-unit-tests` on my pipeline.
1. `--generate-unit-tests` will mistakenly crea…
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I cloned the repository in my Unix terminal with
```
git clone git@github.com:pradumnpc/EMBL_Tranee_assignment.git
```
navigated to `Assignment/snakemake` and run `snakemake -j1`. Got this:
```
…
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I followed all the steps in the usecase directory to run the snakemake but it's failing.
```
./downloadData.sh: 7: Syntax error: "(" unexpected
snakemake -j2 --use-conda
Building DAG of jobs..…
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Mentioned in #37 in this [comment](https://github.com/WayScience/CytoSnake/pull/37#discussion_r1160670160)
The script design is unnecessarily complex, since we are only using a single function call…
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Dear snparcher developers,
I encounter errors when I run the pipeline on real size datasets.
I get this kind of message during bam2gvcf, gvcf2DB, DB2vcf or concat_gvcfs.
```
Error in rule DB2…
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Maybe using snakemake, automate the building of all internal databases. Options should include `--all`, or `--`.
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**Snakemake version**
7.21.0
**Describe the bug**
Snakemake rule to create a kaiju database (https://github.com/bioinformatics-centre/kaiju) ends with error. The same command run successfully…