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The workflow seems to fail quickly on the IRIDA web application side and the Galaxy log suggests staramr is failing due to a problem executing tool: dataset_collections:
`There was a failure execu…
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![snippy4](https://user-images.githubusercontent.com/5425346/54983830-431b1000-4fb6-11e9-906c-1ffcb1e3f703.png)
## Describe the bug
I have created a pipeline plugin and deployed it to an IRIDA insta…
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## Bug report
Hello,
I submitted a `Nextflow` workflow to our cluster (`SLURM` scheduler), but `Nextflow` did not terminate after all tasks were completed. It eventually timed out because of the …
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Error due to `interval.list` instead of `interval_list` suffix
Link: https://gatk.broadinstitute.org/hc/en-us/community/posts/360056676692-HS-PENALTY-20X-is-1-on-one-version-of-GATK-crashes-on-newe…
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__Terms:__
I've annotated each link using the following terms below. I've provided explanations for what I mean by each term.
[Formatting Issues] Usually an issue with bullet or numbered lists
[M…
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https://github.com/bioinformatics-ua/dicoogle/blob/9d612ad883c4310e50a14fd382a0af56a2e8f2ed/dicoogle/src/main/java/pt/ua/dicoogle/server/SearchDicomResult.java#L310
It is necessary to change the enco…
Ilia1 updated
3 years ago
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User report:
Ran with the most recent version of gatk4.1.4.1.
**COMMAND: gatk GenotypeConcordance -R /data/BIOINFORMATICS/REFERENCES/GATK_TEST/resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta -…
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Add the following link to the error message if any system requirement is not met:
https://md-anderson-bioinformatics.github.io/NGCHM-R/articles/Installation.html
For instance, add message to user …
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As discussed at the HUPO Busan Bioinformatics Hub, it would be great to compile a list of all the available mzML (and mzMLb?) parsers for different programming languages.
Off the top of my head and…
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When running samples with the -3 option, VarDictJava seems to return nonsensical output for some deletions. In the attached examples, when processed without -3, the variant is marked as being located…