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Fix bbsplit index staging by using symlinks #1631

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Merged
pinin4fjords merged 2 commits into from
Nov 25, 2025
Merged

Fix bbsplit index staging by using symlinks #1631

pinin4fjords merged 2 commits into from
Nov 25, 2025
+14 −15

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@pinin4fjords pinin4fjords commented Nov 25, 2025

Summary

  • Replaces full directory copy with symlinks when using pre-built bbsplit indices
  • Only copies summary.txt files that need modification, symlinking all other index files
  • Reduces disk usage and improves performance for pre-built index workflows

Test plan

  • Run pipeline with --bbsplit_index pointing to a pre-built index
  • Verify bbsplit runs successfully without timestamp errors
  • Confirm index files are properly symlinked rather than copied

🤖 Generated with Claude Code

pinin4fjords and others added 2 commits November 25, 2025 18:28
@pinin4fjords @claude
Fix bbsplit index staging by using symlinks instead of full copy
6927e31 
Use symlinks for index files instead of copying the entire directory,
only copying summary.txt files that need modification. This reduces
disk usage and improves performance when using pre-built indices.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>
@pinin4fjords @claude
Update CHANGELOG.md for PR #1631
0877ff1 
🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>
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github-actions bot commented Nov 25, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0877ff1

+| ✅ 284 tests passed       |+
#| ❔   8 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   9 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • 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!
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/rnaseq/rnaseq/subworkflows/local/prepare_genome/main.nf: _ versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
    _

❔ Tests ignored:

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2025-11-25 19:41:13

@pinin4fjords pinin4fjords added this to the 3.22.0 milestone Nov 25, 2025
@pinin4fjords pinin4fjords merged commit f7fedf7 into dev Nov 25, 2025
88 of 96 checks passed
@pinin4fjords pinin4fjords deleted the another_bbsplit_fix branch November 25, 2025 20:03
@pinin4fjords pinin4fjords mentioned this pull request Nov 26, 2025
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@FriederikeHanssen FriederikeHanssen mentioned this pull request Nov 26, 2025
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@maxulysse maxulysse maxulysse approved these changes

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