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adds channels to meme mt align #582

Merged
merged 1 commit into from
Jul 4, 2024
Merged

adds channels to meme mt align #582

merged 1 commit into from
Jul 4, 2024

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jemten
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@jemten jemten commented Jul 4, 2024

The MT alignment with bwa meme lacked the newly introduced channels val_mbuffer_mem and val_sort_threads.

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/raredisease 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>).
  • Ensure the test suite passes (nextflow run . -profile test_one_sample,docker --outdir <OUTDIR>).
  • 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).

@jemten jemten marked this pull request as ready for review July 4, 2024 10:09
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github-actions bot commented Jul 4, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ae446ec

+| ✅ 185 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_dark.png
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-07-04 10:09:09

ramprasadn
ramprasadn approved these changes Jul 4, 2024
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Good catch!

@jemten jemten merged commit af42f38 into dev Jul 4, 2024
6 checks passed
@jemten jemten deleted the fix_mt_meme branch July 4, 2024 11:31
@ramprasadn ramprasadn restored the fix_mt_meme branch July 4, 2024 11:52
@ramprasadn ramprasadn deleted the fix_mt_meme branch July 4, 2024 11:52
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@ramprasadn ramprasadn ramprasadn approved these changes

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@jemten @ramprasadn