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Sep 25, 2024
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Improve documentation for Bracken ignore errorStrategy #532

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Add explanation for the Bracken ignore errorSrategy
jfy133 Sep 20, 2024
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Add changelgo
jfy133 Sep 20, 2024
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Fix github handle
jfy133 Sep 20, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

- [#518](https://github.com/nf-core/taxprofiler/pull/518) Fixed a bug where Oxford Nanopore FASTA input files would not be processed (❤️ to @ikarls for reporting, fixed by @jfy133)
- [#523](https://github.com/nf-core/taxprofiler/pull/523) Removed hardcoded `-m lca` from GANON_CLASSIFY due to more options in new version of ganon (fixed by @LilyAnderssonLee & @jfy133)
- [#532](https://github.com/nf-core/taxprofiler/pull/532) - Added missing documentation behind the 'ignore' BRACKEN_BRACKEN error strategy (❤️ to @Mavti for reporting, fixed by @jfy133)

### `Dependencies`

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28 changes: 25 additions & 3 deletions docs/usage/faq-troubleshooting.md
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@@ -1,9 +1,31 @@
# Troubleshooting and FAQs

## I get a warning during centrifuge_kreport process with exit status 255
## I get a warning during CENTRIFUGE_KREPORT or KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE process with exit status 255

When a sample has insufficient hits for abundance estimation, the resulting `report.txt` file will be empty.

When trying to convert this to a kraken-style report, the conversion tool will exit with a status code `255`, and provide a `WARN`.
When trying to convert this to a kraken-style report or merging together, the tools will exit with a status code `255`, and provide a `WARN`.

This is _not_ an error nor a failure of the pipeline, just your sample has no hits to the provided database when using centrifuge.
This is _not_ an error nor a failure of the pipeline, just your sample has no hits to the provided database when using Centrifuge.

## Why does any error or failed process from BRACKEN_BRACKEN get ignored?

If Kraken2 doesn't classify any reads (100% unclassified) Bracken will fail on that input.
Having no reads taxonomically classified can be a reasonable outcome for some samples, and we don't want to treat this as an error.

Therefore to allow the remainder of a given run to complete if a single Bracken task fails, [we set the Nextflow `errorStrategy` to `ignore`](https://github.com/nf-core/taxprofiler/blob/5d3ee5513a84f92773c8376c55b5f4da39835307/conf/base.config#L61-L63).
You will still get a warning in the Nextflow console output and log that a Bracken task failed.

If you want to change this behaviour, you can override the `errorStrategy` in your own Nextflow configuration file.

For example:

```nextflow
process {
withName: BRACKEN_BRACKEN {
errorStrategy = 'retry'
}
}
```

Other `errorStrategy` options can be found on the [Nextflow documentation](https://www.nextflow.io/docs/latest/process.html#errorstrategy).