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Use R1/R2 suffixes in amplicon input fastq file renaming #100

Merged
merged 1 commit into from
Jun 27, 2024
Merged

Use R1/R2 suffixes in amplicon input fastq file renaming #100

merged 1 commit into from
Jun 27, 2024

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fbdtemme
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Description

Use _R1/_R2 suffixes in amplicon input fastq file renaming instead of _1/_2
This ensures limited backward compatibility when using the pipeline with older pixelator containers (<0.17) using the --pixelator_container flag.

@fbdtemme
Use R1/R2 suffixes in amplicon input fastq file renaming
ca32765 
This ensures limited backward compatibility when using the pipeline with older pixelator containers (<0.17) using the `--pixelator_container` flag.
@fbdtemme fbdtemme requested a review from ambarrio June 27, 2024 09:57
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github-actions bot commented Jun 27, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ca32765

+| ✅ 202 tests passed       |+
#| ❔   3 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 2024-06-27 09:57:38

@fbdtemme fbdtemme merged commit 9ea493a into nf-core:dev Jun 27, 2024
4 checks passed
@fbdtemme fbdtemme deleted the tweak-amplicon-renaming branch July 5, 2024 13:37
@fbdtemme fbdtemme mentioned this pull request Jul 15, 2024
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

@ambarrio ambarrio Awaiting requested review from ambarrio

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@fbdtemme @FriederikeHanssen