nf-core/taxprofiler

Add `--add-rank-lineage` to `taxpasta merge` and `taxpasta standardise`

Closed this issue · 1 comments

MajoroMask commented

Description of feature

Hi @jfy133 and all.

In taxpasta output file, we have:

  • tax id by default, --add-name to show tax name, and --add-rank to show tax rank.
  • --add-id-lineage to lineage tax ids, --add-lineage to add lineage tax names.

Adding a --add-rank-lineage to show lineage tax rank information looks natural to me. I've wrote a R script to generate this kind of information from a kraken2 reference inspect file (kraken2 inspect docs) before, so I think this is doable via NCBI taxdump.

MajoroMask commented

Sorry guys, I submitted this issue in the wrong repo. I moved it to taxprofiler/taxpasta#126 and I'll close this one.

  • 👍1