I am not sure of the taxlevels, that seems quite different between bacteria/eukaryota.
edit: Changed to "Domain (replacing Kingdom), Supergroup, Division, Subdivision (new taxonomic rank added), Class, Order, Family, Genus, and Species", should be fine now.
Additionally, I am not sure whether that is compatible with sbdiexport? It seems to me because it was running fine with test.config.
edit: Answer is no -> removed "pr2" from list of compatible DBs because it links to pr2=5.0.0 now
PR checklist
[x] This comment contains a description of changes (with reason).
[ ] If you've fixed a bug or added code that should be tested, add tests!
[ ] If you've added a new tool - have you followed the pipeline conventions in the contribution docs- [ ] If necessary, also make a PR on the nf-core/ampliseq branch on the nf-core/test-datasets repository.
[x] Make sure your code lints (nf-core lint).
[ ] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
[ ] Usage Documentation in docs/usage.md is updated.
[ ] Output Documentation in docs/output.md is updated.
[x] CHANGELOG.md is updated.
[ ] README.md is updated (including new tool citations and authors/contributors).
Closes https://github.com/nf-core/ampliseq/issues/588
I am not sure of the
taxlevels
, that seems quite different between bacteria/eukaryota. edit: Changed to "Domain (replacing Kingdom), Supergroup, Division, Subdivision (new taxonomic rank added), Class, Order, Family, Genus, and Species", should be fine now.Additionally, I am not sure whether that is compatible with sbdiexport? It seems to me because it was running fine with
test.config
. edit: Answer is no -> removed "pr2" from list of compatible DBs because it links to pr2=5.0.0 nowPR checklist
nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).