Update unite to version 9.0

jtangrot commented 1 year ago

UNITE databases are updated to version 9.0, and for qiime version 8.3 is also added. However, I cannot make unite-fungi 9.0 work with qiime (unite-alleuk 9.0 works fine), so I skipped that one for now in the interest of having updated UNITE databases for assignTaxonomy and sintax.

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).
[x] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
[ ] Usage Documentation in docs/usage.md is updated.
[x] Output Documentation in docs/output.md is updated.
[ ] CHANGELOG.md is updated.
[ ] README.md is updated (including new tool citations and authors/contributors).

github-actions[bot] commented 1 year ago

`nf-core lint` overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit c6b8348

+| ✅ 157 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   2 tests had warnings |!

### :heavy_exclamation_mark: Test warnings: * [readme](https://nf-co.re/tools-docs/lint_tests/readme.html) - README did not have a Nextflow minimum version badge. * [schema_lint](https://nf-co.re/tools-docs/lint_tests/schema_lint.html) - Parameter `input` is not defined in the correct subschema (input_output_options) ### :grey_question: Tests ignored: * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `conf/igenomes.config` ### :white_check_mark: Tests passed: * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.gitattributes` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.gitignore` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.nf-core.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.editorconfig` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.prettierignore` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - 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jtangrot commented 1 year ago

This PR addresses issue #574

jtangrot commented 1 year ago

The pacbio_its test probably fails due to out of memory in the assignTaxonomy step. I could either specify unite-fungi=8.3 in the test config, or instead try to increase max_memory in the config file. Which option is preferred?

d4straub commented 1 year ago

However, I cannot make unite-fungi 9.0 work with qiime (unite-alleuk 9.0 works fine), so I skipped that one for now in the interest of having updated UNITE databases for assignTaxonomy and sintax.

agreed edit: actually, why not add unite-fungi 9.0 for QIIME as well but skip sh files (if thats the problem)

I could either specify unite-fungi=8.3 in the test config, or instead try to increase max_memory in the config file. Which option is preferred?

better use unite-fungi=8.3, we do not want to mess with nf-core max resource settings, might lead to more problems.

jtangrot commented 1 year ago

However, I cannot make unite-fungi 9.0 work with qiime (unite-alleuk 9.0 works fine), so I skipped that one for now in the interest of having updated UNITE databases for assignTaxonomy and sintax.

agreed edit: actually, why not add unite-fungi 9.0 for QIIME as well but skip sh files (if thats the problem)

No, the sh files are not the problem, those are only used together with / after assignTaxonomy. It's the qiime formatted database that misbehaves in some way ("this classifier does not support confidence values"), or I am doing something wrong. Also see comment in issue 574.

I could either specify unite-fungi=8.3 in the test config, or instead try to increase max_memory in the config file. Which option is preferred?

better use unite-fungi=8.3, we do not want to mess with nf-core max resource settings, might lead to more problems.

OK, thanks!

jtangrot commented 1 year ago

Thanks!

nf-core / ampliseq