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Add alternative trimmer: AdapterRemoval#285

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jfy133 merged 6 commits intonf-core:devfrom
jfy133:adapterremoval
Mar 24, 2022
Merged

Add alternative trimmer: AdapterRemoval#285
jfy133 merged 6 commits intonf-core:devfrom
jfy133:adapterremoval

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@jfy133 jfy133 commented Mar 23, 2022 •
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PR checklist

Fixes #284

Will require nf-core/test-datasets#482 to be merged before test_adapterremoval works

  • 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/mag 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).

@jfy133 jfy133 added the WIP Work in progress label Mar 23, 2022
@jfy133 jfy133 marked this pull request as draft March 23, 2022 07:46
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github-actions Bot commented Mar 23, 2022

This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @jfy133,

It looks like this pull-request is has been made against the jfy133/nf-core-mag master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the jfy133/nf-core-mag dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@jfy133 jfy133 changed the base branch from master to dev March 23, 2022 07:46
@jfy133 jfy133 marked this pull request as ready for review March 23, 2022 13:39
@jfy133 jfy133 removed the WIP Work in progress label Mar 23, 2022
@jfy133 jfy133 requested review from d4straub and skrakau and removed request for d4straub March 23, 2022 13:40
@jfy133 jfy133 changed the title Adapterremoval Add alternative trimmer: AdapterRemoval Mar 23, 2022
d4straub
d4straub reviewed Mar 24, 2022
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Looks all good apart from a few cosmetic changes and the not running tests (the latter is important I guess).

Comment thread CHANGELOG.md Outdated
Comment thread conf/modules.config Outdated
Comment thread docs/output.md Outdated
Comment thread workflows/mag.nf Outdated
Comment thread workflows/mag.nf Outdated
@jfy133 jfy133 requested a review from d4straub March 24, 2022 10:58
@jfy133 jfy133 merged commit 54e2455 into nf-core:dev Mar 24, 2022
d4straub
d4straub approved these changes Mar 24, 2022
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LGTM!

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@d4straub d4straub d4straub approved these changes

@skrakau skrakau Awaiting requested review from skrakau

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Add AdapterRemoval as alternative clipping tool

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@jfy133 @d4straub