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Replace CSVTK_JOIN to improve processing in large amount of files #486

Merged
merged 10 commits into from
Dec 12, 2024
Merged

Replace CSVTK_JOIN to improve processing in large amount of files #486

merged 10 commits into from
Dec 12, 2024

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atrigila
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@atrigila atrigila commented Dec 9, 2024 •
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PoC: Pivot tables to improve processing of large files.
#484

  • Pivot longer, concat and pivot wider:1000 files (30000 rows each). (duration: 35m 35s)

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/smrnaseq branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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).

@atrigila atrigila self-assigned this Dec 9, 2024
@grst grst self-requested a review December 12, 2024 14:11
@grst grst marked this pull request as ready for review December 12, 2024 14:11
grst
grst approved these changes Dec 12, 2024
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LGTM

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grst commented Dec 12, 2024

The changelog still needs to be updated, then feel free to merge :)

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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.0.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

@atrigila atrigila merged commit 411a499 into nf-core:dev Dec 12, 2024
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@grst grst grst approved these changes

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