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Update several modules #335

Merged
merged 2 commits into from
Jan 31, 2024
Merged

Update several modules #335

merged 2 commits into from
Jan 31, 2024

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jasmezz
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@jasmezz jasmezz commented Jan 31, 2024

Update diverse nf-core/modules, incl:

  • MultiQC 1.18 -> 1.19
  • Add some stub tests + nf-tests
  • Fix some typos/broken URL

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/funcscan 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).

@jasmezz jasmezz requested a review from a team January 31, 2024 15:03
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github-actions bot commented Jan 31, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 1885f0f

+| ✅ 205 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   1 tests had warnings |!
-| ❌  15 tests failed       |-

❌ Test failures:

  • files_exist - File must be removed: lib/nfcore_external_java_deps.jar
  • nextflow_config - Config default value incorrect: params.annotation_prokka_evalue is set as 1e-06 in nextflow_schema.json but is 0.000001 in nextflow.config.
  • nextflow_config - Config default value incorrect: params.amp_ampcombi_cutoff is set as 0.4 in nextflow_schema.json but is 0 in nextflow.config.
  • nextflow_config - Config default value incorrect: params.arg_amrfinderplus_identmin is set as -1.0 in nextflow_schema.json but is -1 in nextflow.config.
  • nextflow_config - Config default value incorrect: params.arg_deeparg_alignmentevalue is set as 1e-10 in nextflow_schema.json but is 1E-10 in nextflow.config.
  • nextflow_config - Config default value incorrect: params.bgc_gecco_pfilter is set as 1e-09 in nextflow_schema.json but is 1E-9 in nextflow.config.
  • files_unchanged - .github/workflows/branch.yml does not match the template
  • files_unchanged - .github/workflows/linting_comment.yml does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • files_unchanged - assets/email_template.html does not match the template
  • files_unchanged - assets/email_template.txt does not match the template
  • files_unchanged - assets/nf-core-funcscan_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-funcscan_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-funcscan_logo_dark.png does not match the template
  • files_unchanged - pyproject.toml does not match the template

❗ Test warnings:

  • 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:

✅ Tests passed:

Run details

  • nf-core/tools version 2.12
  • Run at 2024-01-31 15:04:49

@jasmezz jasmezz merged commit 0ffba22 into dev Jan 31, 2024
15 of 16 checks passed
@jasmezz jasmezz deleted the update-modules branch January 31, 2024 16:41
@jasmezz jasmezz self-assigned this Jan 31, 2024
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@jfy133 jfy133 jfy133 approved these changes

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@jasmezz @jfy133