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Update doc related to simpleaf, alevin-fry and salmon. #368

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merged 5 commits into from
Sep 24, 2024
Merged

Update doc related to simpleaf, alevin-fry and salmon. #368

merged 5 commits into from
Sep 24, 2024

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an-altosian
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In #361, I promised that I would update the doc related to simpleaf, alevin-fry and salmon. Here you go. ;)

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Dongze

@an-altosian an-altosian changed the title Dev Update doc related to simpleaf, alevin-fry and salmon. Sep 16, 2024
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github-actions bot commented Sep 16, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 973508b

+| ✅ 204 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-09-16 03:37:34

@DongzeHE DongzeHE requested review from fmalmeida, heylf and grst and removed request for fmalmeida and heylf September 22, 2024 22:56
fmalmeida
fmalmeida approved these changes Sep 23, 2024
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I think it looks neat, I have only one genuine question. Othewise, it LGTM.

CITATIONS.md
* [Alevin-fry](https://doi.org/10.1038/s41592-022-01408-3)

> He, D., Zakeri, M., Sarkar, H. et al. Alevin-fry unlocks rapid, accurate and memory-frugal quantification of single-cell RNA-seq data. Nat Methods 19, 316–322 (2022).

* [Alevin](https://doi.org/10.1186/s13059-019-1670-y)
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Is alevin still relevant here? Is alevin-fry totally different or it uses alevin?

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@an-altosian an-altosian Sep 23, 2024 •
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Conceptually, alevin is definitely relevant here. As the module in salmon for single-cell data quantification, it is the predecessor of alevin-fry and the work where alevin-fry is build upon. So, although the alevin-fry workflow does not directly call the salmon alevin module for read quantification, I would suggest to keep the citation here ;). Thanks!

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perfect

@DongzeHE DongzeHE merged commit 3e2412d into nf-core:dev Sep 24, 2024
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@fmalmeida fmalmeida fmalmeida approved these changes

@grst grst Awaiting requested review from grst

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@an-altosian @fmalmeida @DongzeHE