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Fix bowtie index issue #317

Merged
merged 11 commits into from
Feb 21, 2024
Merged

Fix bowtie index issue #317

merged 11 commits into from
Feb 21, 2024

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christopher-mohr
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@christopher-mohr christopher-mohr commented Feb 16, 2024 •
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This

  • fixes the access of the bowtie index (index not defined).

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/smrnaseq 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 Feb 16, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit bf78343

+| ✅ 174 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   1 tests had warnings |!
-| ❌   8 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/WorkflowSmrnaseq.groovy
  • 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 - pyproject.toml does not match the template

❗ Test warnings:

❔ Tests ignored:

  • nextflow_config - Config default ignored: params.fastp_known_mirna_adapters

✅ Tests passed:

Run details

  • nf-core/tools version 2.13
  • Run at 2024-02-21 11:17:56

@christopher-mohr christopher-mohr added the WIP Work in progress label Feb 16, 2024
@christopher-mohr
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We should still add a test with specified bowtie index path before merging

@apeltzer apeltzer merged commit ad7af7a into nf-core:dev Feb 21, 2024
9 of 10 checks passed
@christopher-mohr christopher-mohr deleted the fix_bowtie_index_issue branch February 21, 2024 16:09
@apeltzer apeltzer mentioned this pull request Feb 22, 2024
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@apeltzer apeltzer apeltzer approved these changes

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