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Issue797 skip umitools extract #807

Merged
merged 10 commits into from
Apr 29, 2022
Merged

Issue797 skip umitools extract #807

merged 10 commits into from
Apr 29, 2022

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MatthiasZepper
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@MatthiasZepper MatthiasZepper commented Apr 25, 2022 •
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Add --skip_umi_extract to account for pre-existing UMIs header embeddings. #797

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/rnaseq 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.
  • [x ] CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@MatthiasZepper MatthiasZepper added help wanted Extra attention is needed WIP Work in progress labels Apr 25, 2022
@drpatelh
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How are we doing here @MatthiasZepper ? Need any help/comments? Going to try and get any new enhancements in before end of day for testing before release. Lemme know :) Thanks for volunteering here! :bowtie:

@MatthiasZepper MatthiasZepper force-pushed the issue797-skip_umitools_extract branch from e53ac90 to fa4b6df Compare April 29, 2022 09:29
@MatthiasZepper MatthiasZepper marked this pull request as ready for review April 29, 2022 10:51
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github-actions bot commented Apr 29, 2022 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit b5981a3

+| ✅ 144 tests passed       |+
#| ❔   3 tests were ignored |#

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.3.2
  • Run at 2022-04-29 13:48:00

drpatelh
drpatelh reviewed Apr 29, 2022
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drpatelh
drpatelh approved these changes Apr 29, 2022
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Awesome! Thanks a bunch @MatthiasZepper !

@drpatelh
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Will run tests again on follow-up PRs so merging.

@drpatelh drpatelh merged commit ee5b7f6 into nf-core:dev Apr 29, 2022
@drpatelh drpatelh mentioned this pull request Apr 29, 2022
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@MatthiasZepper MatthiasZepper deleted the issue797-skip_umitools_extract branch April 29, 2022 16:16
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