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first commit msstatistics csv -> parquet [DO NOT MERGE]#391

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ypriverol merged 41 commits intobigbio:devfrom
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Aug 3, 2024
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first commit msstatistics csv -> parquet [DO NOT MERGE]#391
ypriverol merged 41 commits intobigbio:devfrom
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@ypriverol ypriverol commented Jul 29, 2024

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/quantms branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • 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).

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github-actions bot commented Jul 29, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit c3511c9

+| ✅ 292 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!
Details

❗ Test warnings:

  • nfcore_yml - nf-core version not set in .nf-core.yml

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-03 22:55:37

@ypriverol ypriverol changed the title first commit msstatistics csv -> parquet first commit msstatistics csv -> parquet [DO NOT MERGE] Jul 29, 2024
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ypriverol commented Jul 29, 2024

Pending of https://github.com/bigbio/quantms-utils/pulls and also future release of the package.

This was linked to issues Jul 30, 2024
Use compressed parquet files for mzml statistics #390
Closed
Update the pipeline to SDRF validation 0.0.28 #392
Closed
@ypriverol ypriverol mentioned this pull request Jul 30, 2024
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@ypriverol ypriverol requested a review from daichengxin August 2, 2024 22:46
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jpfeuffer commented Aug 3, 2024

Cool. Looks like we are down from 3.5 to 1.3 GB for the DIA test

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ypriverol commented Aug 3, 2024

Cool. Looks like we are down from 3.5 to 1.3 GB for the DIA test

We still have the issue with mamba and micromamba tests.

@ypriverol ypriverol merged commit 32a4a39 into bigbio:dev Aug 3, 2024
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jpfeuffer commented Aug 4, 2024 •
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I think it's ok if you skip them for now. I will check if there is a solution by now. It was always a flaky test due to the multiple processes that try to create/change conda environments.

Or does it fail because sth else? No, right?

@ypriverol ypriverol mentioned this pull request Aug 5, 2024
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Update the pipeline to SDRF validation 0.0.28 Use compressed parquet files for mzml statistics

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