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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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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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I'm trying to run a workflow with subworkflows with the `--forceall` flag specified.
Expected behavior: subworkflow rebuild all rules.
Actual behavior: subworkflows don’t rebuild any rule if the…
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Hi,
I have been trying to run the chip-seq workflow of seq2science. It starts but stops when 7% of the jobs are done.
```
seq2science --version
seq2science: v0.5.1
```
**To Reproduce**
Plea…
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![Screenshot 2023-11-14 at 5 43 08 PM](https://github.com/gao-lab/GLUE/assets/6439736/0f0c7ded-5954-4347-a339-fa4019792497)
I have just configured the conda and when I try to run evaluation on GP…
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i was executing the code example given in the github page
this is my code:
run-ntedit polish --draft filt_contig_assembly.fa --reads filtered_P1 -k 71 -t 8
but it is showing an error and based…
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**Snakemake version**
7.31.0
**Describe the bug**
Take 3 rules (none set threads or resources unless noted):
- Rule 1 outputs using `pipe()`
- Rule 2 consumes the pipe from rule 1, sets `re…
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- [x] I've checked [docs](https://rich.readthedocs.io/en/latest/introduction.html) and [closed issues](https://github.com/Textualize/rich/issues?q=is%3Aissue+is%3Aclosed) for possible solutions.
- [x…
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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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When using `--restart-times`, the log file is instantly deleted after an attempt fails, so the user cannot look at the log file to see what went wrong. The user must instead wait until the last attemp…