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Multiple mithocondial/plastid genomes crashes ataqv #262

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maltesemike opened this issue Feb 20, 2023 · 3 comments
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Multiple mithocondial/plastid genomes crashes ataqv #262

maltesemike opened this issue Feb 20, 2023 · 3 comments
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2.1

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maltesemike commented Feb 20, 2023 •
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Description of the bug

Plants and algae have chloroplast genomes in addition to a mithocondrial genome, so multiple names need to be provided in the params file. A work around was to provide multiple names that are separated by a | symbol, but unfortunately the pipeline crashes on the ataqv step as this is not recognised under the --mitochondrial-reference-name flag.

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@maltesemike maltesemike added the bug Something isn't working label Feb 20, 2023
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JoseEspinosa commented Jun 27, 2023 •
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Cross reference to Slack discussion: https://nfcore.slack.com/archives/CE5EL6326/p1653999167419739

@JoseEspinosa JoseEspinosa self-assigned this Jun 27, 2023
@JoseEspinosa JoseEspinosa added this to the 2.1 milestone Jun 27, 2023
@JoseEspinosa JoseEspinosa mentioned this issue Jun 28, 2023
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@JoseEspinosa JoseEspinosa added WIP Work in progress and removed WIP Work in progress labels Jun 28, 2023
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A new parameter ataqv_mito_reference should allow you know to directly set the ataqv --mitochondrial-reference-name flag separately from the mito_name so that ataqv does not crash. If you want to give it a try it is available in the dev version of the pipeline.

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Available in v2.1.0

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