Update nextclade rules in ingest [#21]

[genehack]

Description of proposed changes

Updates usage of augur in ingest build to align with pathogen repo guide standards.

Closes #21

• Checks pass

[victorlin]

Is there a reason to mark this as temp? Would it not be useful for debugging along with all the other intermediate files in results/?

[genehack]

It's marked as temp because the next rule (join_metadata_and_nextclade) merges this file and the other metadata (data/subset_metadata.tsv) together, so all the data ends up in that file anyway. Any debugging would most likely happen using that file.

[victorlin]

What if we want to debug augur curate rename in this rule and join_metadata_and_nextclade fails or we simply don't want to run it?

My argument is mostly based on consistency, since the same could be said about results/nextclade.tsv: why not make that temp because it eventually makes its way into results/metadata.tsv?

Consider this non-blocking since it works fine.

[tsibley]

What if we want to debug augur curate rename in this rule and join_metadata_and_nextclade fails or we simply don't want to run it?

In such a situation, Snakemake's --notemp option could be used.

[genehack]

My argument is mostly based on consistency, since the same could be said about results/nextclade.tsv: why not make that temp because it eventually makes its way into results/metadata.tsv?

results/nextclade.tsv and results/nextclade_metadata.tsv are effectively isotopes of the same underlying data; we don't need to retain both of them, because if you have one, you can tell what had to have been in the other one. I marked the latter one as temp because it's the newer of the two, so it was less change.