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bwa should use -Y and not -M #644

Merged
merged 3 commits into from
Jul 17, 2022
Merged

bwa should use -Y and not -M #644

merged 3 commits into from
Jul 17, 2022

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FriederikeHanssen
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@FriederikeHanssen FriederikeHanssen commented Jul 17, 2022 •
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close #101

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 - add to the software_versions process and a regex to scrape_software_versions.py
    • 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).
  • 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).

@maxulysse
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Should we look into similar settings fro dragmap?

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github-actions bot commented Jul 17, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f5f49ea

+| ✅ 145 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.

❔ Tests ignored:

  • 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: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-07-17 10:38:19

@FriederikeHanssen
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Should we look into similar settings fro dragmap?

yes, good point

@FriederikeHanssen
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the command used for dragmap is the most basic one according to the docs. Couldn't find something simialr as for the bwa yet. Maybe for now the basic command is fine and we keep an eye on the developments there

@maxulysse maxulysse merged commit d2388d1 into nf-core:dev Jul 17, 2022
@FriederikeHanssen FriederikeHanssen mentioned this pull request Jul 17, 2022
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@maxulysse maxulysse maxulysse approved these changes

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@FriederikeHanssen @maxulysse