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Fixing less than 1000 reads issue #77

Merged
merged 3 commits into from
Mar 11, 2024
Merged

Fixing less than 1000 reads issue #77

merged 3 commits into from
Mar 11, 2024

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asp8200
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@asp8200 asp8200 commented Feb 21, 2024 •
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Fixing #22.

Tested manually:

  1. on bam-file with more than 1000 reads paired end (using -profile test),
  2. on bam-file with less than 1000 reads all of which are paired, and
  3. on bam-file with less than 1000 reads including a couple of reads that are not paired.

As far as I understand, in the instruction samtools view $reference $input -@$task.cpus | head -n1000, samtools will read/parse at most 1000 lines from the input-bam, and that is what we want. We don't want samtools to spend time reading all reads from huge bam-files.

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github-actions bot commented Feb 21, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 767a274

+| ✅ 168 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   6 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 2.1.0
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file
  • 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:

  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-03-11 13:37:34

@asp8200 asp8200 marked this pull request as ready for review February 21, 2024 09:55
@maxulysse maxulysse changed the title Fixing #22 Fixing less than 1000 reads issue Mar 11, 2024
@maxulysse maxulysse merged commit 0c02877 into nf-core:dev Mar 11, 2024
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@maxulysse maxulysse maxulysse approved these changes

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@asp8200 @maxulysse