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Change .bai index for .csi index in samtools_index #391

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merged 5 commits into from
Aug 27, 2024
Merged

Change .bai index for .csi index in samtools_index #391

merged 5 commits into from
Aug 27, 2024

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atrigila
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@atrigila atrigila commented Aug 27, 2024 •
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Fixes #132

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!
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • CHANGELOG.md is updated.

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github-actions bot commented Aug 27, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ff5ace9

+| ✅ 214 tests passed       |+
#| ❔   1 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:

  • nextflow_config - Config default ignored: params.fastp_known_mirna_adapters

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-27 13:43:23

@atrigila atrigila marked this pull request as ready for review August 27, 2024 14:54
@atrigila atrigila self-assigned this Aug 27, 2024
apeltzer
apeltzer approved these changes Aug 27, 2024
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That doesnt have any unforeseen side effects? In the past I sometimes had other tools using samtools indices that went awkward when being supplied with a CSI index. But ok, the tests run fine 👍🏻

nschcolnicov
nschcolnicov approved these changes Aug 27, 2024
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LGTM

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That doesnt have any unforeseen side effects? In the past I sometimes had other tools using samtools indices that went awkward when being supplied with a CSI index. But ok, the tests run fine 👍🏻

I took a closer and it makes sense that the changes have no other impact.
Looking at the subworkflow "BAM_SORT_STATS_SAMTOOLS" script: The both the .csi or .bai files that are outputed are then combined with the .bam files channel and then used as input for "BAM_STATS_SAMTOOLS" which produces 3 stat files as output which we are validating with md5sums in the tests. But besides this, the .csi or .bai files emitted by "SAMTOOLS_SORT" are not used for anything else afterwards.

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Exactly :) thanks for having a look

@atrigila atrigila merged commit 17c027e into nf-core:dev Aug 27, 2024
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@atrigila atrigila mentioned this pull request Aug 27, 2024
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Cool then :)

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@nschcolnicov nschcolnicov nschcolnicov approved these changes

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