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Hi,
I am having an issue when pipelining multiple samples with snakemake. It appears that funannotate (e.g. clean) uses the current working directory to store temporary files. These get overwritten…
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What is the best way to edit the .yaml file to use the viral genome analysis sections (assembly/intrahost variation)?
Would input files need to be depleted already?
Which dir would the input file…
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**Snakemake version**
v8.3.7
**Describe the bug**
Attempt to generate a Dockerfile with `snakemake --containerize` fails when the workflow has a global Conda directive.
**Logs**
The following…
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There are a whole bunch of frameworks for organizing research code/computational pipelines, like redun, [WDL](https://github.com/openwdl/wdl), [CWL](https://www.commonwl.org/), [Nextflow](https://www.…
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I created my own chromsize.tsv:
it looks like
Chromosome Start End
0 chr1 0 248956422
1 chr2 0 242193529
2 chr3 0 198295559
3 chr4 0 19…
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Currently, https://github.com/USGS-R/delaware-model-prep/blob/master/Snakefile downloads the geospatial fabric catchment attributes and their metadata, relates catchments to segments, subsets for UMN …
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# Run / system info
I'm running rotary commit 40381cc on Ubuntu 22.04.3, within the snakemake argument `--until circularize` (to run everything up until the start of the annotation module).
# Prob…
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**Snakemake version**
7.31.0
**Describe the bug**
On my local machine, I developed a pipeline with conda envs and it runs.
Now, I wanted to test the pipeline on another machine (server fr…
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Hello, I am new to DROP. We have a single affected sample and hence wanted to use the publicly available control dataset of external counts. First I wanted to test the pipeline to see if I have setup …
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Highlight the challenges you encountered while making a workflow in snakemake