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Registry update for all modules #509

Merged
merged 7 commits into from
Sep 25, 2023
Merged

Registry update for all modules #509

merged 7 commits into from
Sep 25, 2023

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jfy133
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@jfy133 jfy133 commented Sep 15, 2023 •
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Updates the URL to remove the registeries in all teh modules (also repairing a couple of patches)

Should only be merged after #508

TODO

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/mag branch on the nf-core/test-datasets repository.
  • 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.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Sep 15, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b8f07b9

+| ✅ 155 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 2.4.0
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-09-16 18:03:05

d4straub
d4straub approved these changes Sep 18, 2023
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LGTM

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jfy133 commented Sep 21, 2023

Testing...

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jfy133 commented Sep 25, 2023

Confirm pass!

I note that GTDB-TK in the full test does not end up being executed because now the completeness and contamination values do not reach the default thresholds for any of the bins... but this is a separate issue. I assume this occurred since the change of the GTDB database version/tool update a couple of versions ago.

@d4straub do you see any reason why I should not just set those two values to very low for the test_full. At least that way the tool will execute in the full test (even if one wouldn't usually do this).

I guess this was not noticed previously due to the full test failures because of the SPAdes incompatibility with fusion..

@jfy133 jfy133 merged commit 260910d into dev Sep 25, 2023
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@jfy133 jfy133 changed the title [DO NOT MERGE] Registry update for all modules Registry update for all modules Sep 25, 2023
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@d4straub do you see any reason why I should not just set those two values to very low for the test_full. At least that way the tool will execute in the full test (even if one wouldn't usually do this).

As far as I remember GTDB failed with too incomplete bins. GTDB uses marker genes to classify bins and when no marker genes are found it clashed. But that might have changed over time and software updates.

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