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Account for single end reads when splitting fastqs#657

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fastq_split_single_end
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Account for single end reads when splitting fastqs#657
matthdsm wants to merge 1 commit intodevfrom
fastq_split_single_end

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@matthdsm matthdsm commented Jul 19, 2022

Currently, the fastq splitting approach assumes data is always paired end, this takes single ended data into account

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 - add to the software_versions process and a regex to scrape_software_versions.py
    • 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/sarek 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).

@matthdsm matthdsm requested a review from maxulysse as a code owner July 19, 2022 09:03
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matthdsm commented Jul 19, 2022

Also, I'm not really sure if the tokenizing is really necessary. I'm doing the same thing in my pipeline and a simple sort works just as good

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github-actions Bot commented Jul 19, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d8b798d

+| ✅ 146 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!
Details

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-07-19 09:04:48

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maxulysse commented Jul 19, 2022

We only use paired end data in sarek at the moment:

sarek/workflows/sarek.nf

Line 1134 in b0e4873

if (params.step == 'mapping') return [meta, [fastq_1, fastq_2]]

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matthdsm commented Jul 19, 2022

Then I have said nothing! Feel free to close

@maxulysse maxulysse closed this Jul 19, 2022
@matthdsm matthdsm deleted the fastq_split_single_end branch July 19, 2022 09:11
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