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Fix_file_collision_when_using_cellranger #232

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merged 10 commits into from Jun 13, 2023
Merged

Fix_file_collision_when_using_cellranger #232

merged 10 commits into from Jun 13, 2023

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adamrtalbot
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  • When using cellranger, files would collide because they had the same filename. This fix filters to only the relevant files when creating seurat or h5ad files.
  • As a bonus, it should offer a small speed improvement.

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 - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/scrnaseq 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 --outdir <OUTDIR>).
  • 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).

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github-actions bot commented Jun 7, 2023 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit dd6468e

+| ✅ 157 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: '2.3.2'
  • system_exit - System.exit in WorkflowScrnaseq.groovy: System.exit(1) [line 18]

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-06-13 15:21:35

@zvittorio zvittorio mentioned this pull request Jun 8, 2023
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@adamrtalbot adamrtalbot mentioned this pull request Jun 13, 2023
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fmalmeida
fmalmeida approved these changes Jun 13, 2023
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@fmalmeida fmalmeida left a comment

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It looks really good. Even though the changes all make sense and are straightforward, just to be extra sure, did the tests passed?

@adamrtalbot adamrtalbot merged commit c2034fb into dev Jun 13, 2023
14 checks passed
@adamrtalbot adamrtalbot deleted the fix_file_collision_when_using_cellranger branch June 13, 2023 16:29
@adamrtalbot adamrtalbot mentioned this pull request Jun 27, 2023
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@fmalmeida fmalmeida fmalmeida approved these changes

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