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Follow up to https://github.com/nextstrain/ncov-ingest/pull/451.
We are using the Snakemake `--stats` flag to get workflow stats for [GISAID](https://github.com/nextstrain/ncov-ingest/blob/f5f238b…
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Hei it's Yannick again.
As recommended, I started from stratch with the new release and installed micromamba and the newest version of snakemake alongside it.
When trying to do a test run, I immedi…
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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…
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### Current Behavior
`snakemake --cores 1 -pf --configfile config/gisaid.yaml`
Error:
```
download failed: s3://nextstrain-data-private/files/workflows/avian-flu/ha/sequences.fasta.zst to - Unab…
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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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**Snakemake version**
Problem hit testing snakemake 8.16.0 under macOS on ARM, installed via conda. Reproduced using latest snakemake from git.
**Describe the bug**
Snakemake's job solver use…
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To bump all modules to snakemake 8 (#12) we primarily need to document the libraries required to process the initial Snakemake file. These should be added to `envs/global.yaml` and cross-linked into t…
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**Snakemake version** 8.16.0
**Describe the bug**
The default behavior of `cores` is different and limits the number of threads for submitted jobs to the number of cores on the host machine.…
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**Snakemake version**
snakemake-minimal 8.18.0 pyhdfd78af_0 bioconda
**Describe the bug**
snakemake produce Error when using "--max-jobs-per-timespan" switch.
…
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**Is your feature request related to a problem? Please describe.**
Including additional tools in MMEDS should be simply a matter of defining inputs, outputs, and command calls. It is unclear whether …
cleme updated
1 month ago