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### Current Behavior
Invoking `nextstrain build --docker` or (--aws-batch) does not pass `--cores` option to snakemake causing error:
```
Error: you need to specify the maximum number of CPU cores …
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I keep getting this error on my pyshop server when I retrieve the "snakemake" package (e.g. `pip3 install snakemake`). My pip version is `10.0.1`.
```
2018-04-23 19:51:52,401 ERROR [waitress][wait…
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We need to dynamically create a dependency graph based on the input and output files to visualize the progress of the workflows.
Some options we should consider from snakemake
--d3dag, --dag, --ru…
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Noting error in the automated genbank/clade-counts workflow:
- [2024-07-23](https://github.com/nextstrain/forecasts-ncov/actions/runs/10069513692)
- [2024-07-24](https://github.com/nextstrain/foreca…
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As per assembly workflow in Really Quick Copy-And-Paste Quick Start I copied the json file specified and execute the following which gave me the following error:
$ export SINGULARITY_BINDPATH="data:…
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**Snakemake version**:
7.25.4 (but has not been fixed in the main branch, unless I'm misunderstanding something)
**Describe the bug**
When I want to "clean up" a large workflow (e.g. to mark …
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Add benchmarking to every rule
Also write the time to run it all to a log?
[PR-29]
[PR-29]: https://clinicalgenomics.atlassian.net/browse/PR-29
ghost updated
3 years ago
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In Ubuntu os I ran the command from the Really Quick Copy and Paste Quick Start:
snakemake -p --configfile=config/custom_readfilt_workflow.json read_filtering_posttrim_workflow
and received this e…
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Executed the following (my new datafiles were specified in sturner_readfilt_workflow_001x.json):
snakemake -p -n --use-singularity --local-cores 4 --configfile=config/sturner_readfilt_workflow_001x…
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## Description
Entering free text is generally inconvenient and error prone for users. For the "Workflow type" and "Workflow type version" fields in particular, at any time, only a subset of values i…