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```
(/fs/ess/PAS2136/Workshops/Snakemake/conda_env) [thompsonmj@o0647 SnakemakeWorkflow]$ snak
emake -c1 --use-singularity DrexelMetadata/bj373514.json
Building DAG of jobs...
Using shell: /usr/bi…
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Hi,
I am trying to run the UltraQuant workflow on multiple nodes (in parallel mode - like MPI) of a SLURM based cluster. but unfortunately, it keeps giving me fatal I/O errors (files missing relat…
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Currently annotation calling is one of the largest bottlenecks of the pipeline. It is currently split into several rules and accompanying scripts.
Rules
- peak_Transcripts
- peak_ExonIntron
- pe…
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Hello,
First of all, fantastic software! I've been trying it out and it's super cool.
I have a suggestion regarding the output files. As you mention in the README: _files are only created if there i…
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I'm trying to run grist on one sample, using starting with SRA accession numbers (not trying to use local genomes).
Im getting a "`OSError: Generic StreamReadError error`" during `rule kmer_trim_rea…
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The workflows I have been dealing with necessarily seem to result in large DAGs (large reduce step, and many different samples to process). The batch feature can deal with this, but this adds another …
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Snakemake now has flags --preemption-default and --preemptible-rules, that allow to define which rules are eligible for being killed by the cloud provider (which leads to automatic restart). It would …
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E.g.:
```json
{
"@id": ".tests",
"@type": ["Dataset", "TestDefinition"],
}
```
This is useful information even if it's not actionable. We need to relax the "A test definition MUST r…
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**Snakemake version**
v7.20.0 and later
**Describe the bug**
Before v7.20.0, at least up to v7.19.1, it was possible to specify `--jobs all`. This now throws an error, at least when run with `-n`…
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Currently, `pyani-plus` uses different third-party software to compare genomes, and each software handles the order of genomes differently. For example, in `BLAST`, the order is `` then ``, while in `…