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Update README.md - add ref to nf-core/rnaseq and Affymetrix #149

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merged 5 commits into from
Jul 25, 2023
Merged

Update README.md - add ref to nf-core/rnaseq and Affymetrix #149

merged 5 commits into from
Jul 25, 2023

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smoe
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@smoe smoe commented Jul 20, 2023

I found your nf-core libraries via your cut'n'run library, which at the end did not tell me what to do with the scores. And the same then happened to me after I had executed the RNA-seq pipeline. In my mind, both those workflows should prepare for running this differential-abundance one afterwards. I had prepared nf-core/cutandrun#198 with a rough description on how I had tried to make sense of it all (when I did not yet know about this workflow) and have prepared nf-core/rnaseq#1060 to at least provide a link to here.

I can very much understand if you do not want to make workflows inter-dependent at this stage, on a technical level, but some guidance of your users where to go next does not hurt.

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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 @smoe,

It looks like this pull-request is has been made against the smoe/differentialabundance 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 smoe/differentialabundance 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!

@smoe smoe changed the base branch from master to dev July 20, 2023 10:40
pinin4fjords
pinin4fjords reviewed Jul 25, 2023
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github-actions bot commented Jul 25, 2023 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit 6c2582a

+| ✅ 158 tests passed       |+

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-07-25 13:00:10

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@nf-core-bot fix linting

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@smoe thanks for the contribution- I would prefer the updated wording I committed. Could you add a changelog entry under the current 'added' please, following the template you will see used by other entries?

@smoe smoe changed the title Update README.md - aded ref to nf-core/rnaseq and Affymetrix Update README.md - added ref to nf-core/rnaseq and Affymetrix Jul 25, 2023
@smoe smoe changed the title Update README.md - added ref to nf-core/rnaseq and Affymetrix Update README.md - add ref to nf-core/rnaseq and Affymetrix Jul 25, 2023
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smoe commented Jul 25, 2023

Done. Should I also rebase and squash?

pinin4fjords
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pinin4fjords approved these changes Jul 25, 2023
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Looks good now- just merge when the tests pass (no squash/ rebase required).

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smoe commented Jul 25, 2023

I do not have the permissions to merge, please kindly help me out - and also thank you for fixing the wording. I am confident that this will help many people.

The next thing for me, so I thought, would now be to have a look at the documentation and describe in more detail how to transition from the nf-core/rnaseq workflow.

@pinin4fjords pinin4fjords merged commit e452c65 into nf-core:dev Jul 25, 2023
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@smoe smoe deleted the patch-2 branch August 2, 2023 15:38
@pinin4fjords pinin4fjords added this to the 1.3.0 milestone Oct 10, 2023
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