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sbdi-gtdb=R08-RS214-1 (r214) #751

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merged 3 commits into from
Jun 18, 2024
Merged

sbdi-gtdb=R08-RS214-1 (r214) #751

merged 3 commits into from
Jun 18, 2024

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erikrikarddaniel
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@erikrikarddaniel erikrikarddaniel commented Jun 17, 2024 •
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PR checklist

  • 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.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

Finally, last year's release of GTDB in SBDI-GTDB vetted format.

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This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @erikrikarddaniel,

It looks like this pull-request is has been made against the erikrikarddaniel/ampliseq master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the erikrikarddaniel/ampliseq dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@erikrikarddaniel erikrikarddaniel changed the base branch from master to dev June 17, 2024 14:16
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github-actions bot commented Jun 17, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 92f7fda

+| ✅ 281 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-06-18 07:36:20

d4straub
d4straub approved these changes Jun 18, 2024
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LGTM, just one comment.
Also, GTDB release 220 came out in April, maybe we should add that as well

conf/ref_databases.config Outdated
@@ -130,6 +130,14 @@ params {
dbversion = "SBDI-GTDB-R07-RS207-1 (https://scilifelab.figshare.com/articles/dataset/SBDI_Sativa_curated_16S_GTDB_database/14869077/4)"
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Key 'sbdi-gtdb' still leads to Release R07-RS207-1, wouldnt it be good to update it?

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Good catch! I've pushed an update.

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LGTM, just one comment. Also, GTDB release 220 came out in April, maybe we should add that as well

Coming up. I've run my pipeline and produced the files. Now this needs to be submitted for storage and I'm not sure I'll make it before going on vacation next week.

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@d4straub : The test_reftaxcustom fails because https://zenodo.org/record/4310151/files/rdp_species_assignment_18.fa.gz cannot be found. I can't see that this happened with my PR but I also think that I saw all tests pass the other day?

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Several tests use that file, so I assume that was a temporal problem and resumed the test. Hope it will pass ;)

@erikrikarddaniel erikrikarddaniel merged commit a4fc17f into nf-core:dev Jun 18, 2024
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@erikrikarddaniel erikrikarddaniel deleted the sbdi-gtdb-r214 branch June 18, 2024 09:38
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