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.

Command used and terminal output

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Relevant files

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System information

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