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Sarek minimap2 #2

Merged
merged 5 commits into from
Mar 7, 2024
Merged

Sarek minimap2 #2

merged 5 commits into from
Mar 7, 2024

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EgorGuga
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@EgorGuga EgorGuga commented Mar 7, 2024

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/sarek 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).

@EgorGuga EgorGuga merged commit a96a152 into minimap2 Mar 7, 2024
29 of 38 checks passed
@EgorGuga EgorGuga deleted the sarek_minimap2 branch March 7, 2024 12:16
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github-actions bot commented Mar 7, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 62a0798

+| ✅ 176 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   2 tests had warnings |!
-| ❌   9 tests failed       |-

❌ Test failures:

  • files_exist - File must be removed: lib/Utils.groovy
  • files_exist - File must be removed: lib/WorkflowMain.groovy
  • files_exist - File must be removed: lib/NfcoreTemplate.groovy
  • files_exist - File must be removed: lib/WorkflowSarek.groovy
  • files_unchanged - .github/CONTRIBUTING.md does not match the template
  • files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
  • 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

❗ Test warnings:

  • files_exist - File not found: .github/workflows/awstest.yml
  • pipeline_todos - TODO string in WorkflowSarek.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/sarek/sarek/.github/workflows/awstest.yml
  • template_strings - template_strings

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-03-07 12:04:23

EgorGuga pushed a commit that referenced this pull request Apr 25, 2024
@nschcolnicov
Merge pull request #2 from nschcolnicov/tmp
eea2ea0 
Clean up code changes
EgorGuga pushed a commit that referenced this pull request Dec 16, 2024
@alexanderchang1
Merge pull request #2 from alexanderchang1/alexanderchang1-patch-1
524ac6b 
Update CHANGELOG.md
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@EgorGuga