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Fix bwa mem indexing and re-update MQC SeqTools versions after git me… #867

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jfy133 merged 4 commits into from
Mar 24, 2022
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Fix bwa mem indexing and re-update MQC SeqTools versions after git me… #867

jfy133 merged 4 commits into from
Mar 24, 2022

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@jfy133 jfy133 commented Mar 24, 2022 •
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…ss this morning

Also adds test for --skip_collapse with bwa mem to account for the error

fixes #866

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](https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md)
    • If necessary, also make a PR on the nf-core/eager 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).

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@jfy133 jfy133 linked an issue Mar 24, 2022 that may be closed by this pull request
BWA mem fails for paired-end sequencing data that shouldn't be collapsed due to wrong file suffix #866
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@jfy133 jfy133 requested a review from a team March 24, 2022 09:38
@jfy133 jfy133 mentioned this pull request Mar 24, 2022
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maxibor
maxibor approved these changes Mar 24, 2022
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LGTM once CI test is passing

@jfy133 jfy133 merged commit 917557a into dev Mar 24, 2022
@jfy133 jfy133 deleted the bwamem-fix branch March 24, 2022 11:39
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BWA mem fails for paired-end sequencing data that shouldn't be collapsed due to wrong file suffix

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