qiime2/q2-types

Laneless Casava transformers are broken

ebolyen opened this issue · 1 comments

ebolyen commented

Bug Description
When importing a CasavaOneEightLanelessPerSampleDirFmt, the manifest will have the original filenames written (which do not include lane designations). This will not match the archive's filename which will use a default lane number of 1. This will break things downstream.

The path variable in the for loop is what is written, but we want something from a path_maker() call, or even better, write_data() could return the path that was actually written, and then that could be placed into the manifest.

Steps to reproduce the behavior

  1. Import data as CasavaOneEightLanelessPerSampleDirFmt
  2. Observe the internal manifest is in an inconsistent state.

Computation Environment

  • QIIME 2 2019.*

Questions

  1. Should write_data return the path that was written to? This would make the API a little nicer to work with in the transformer.

References

  1. https://forum.qiime2.org/t/file-names-change-when-importing-and-mismatch-manifest/12682
ebolyen commented

fixed in #236