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bokulich-lab / q2-assembly

QIIME 2 plugin for (meta)genome assembly.
BSD 3-Clause "New" or "Revised" License
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BUG: 'meta' preset is allowed by q2-assembly command assemble megahit despite 'meta' not being a preset option for megahit #98

Open schaermi opened 2 months ago

schaermi commented 2 months ago

Describe the bug The documentation for the qiime assembly plugin lists 'meta' as an option for the flag --p-presets. When this option is used, the user receives an error message stating that meta is an invalid preset for megahit.

To Reproduce Steps to reproduce the behavior:

  1. Execute the command qiime assembly assemble-megahit with the flag --p-presets 'meta': qiime assembly assemble-megahit --i-seqs mysequences.qza --p-presets 'meta' --o-contigs mycontigs.qza --verbose
  2. Read stdout and stderr output

Expected behavior I thought 'meta' was a standard preset for metagenomic data in megahit which would produce a .qza artifact containing contigs,

Please complete the following information:

Additional context I encountered this error while working on the Euler cluster.