Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

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

Merged
merged 41 commits into from
Aug 3, 2024
Merged

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

merged 41 commits into from
Aug 3, 2024

Conversation

ypriverol
Copy link
Member

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).

@github-actions GitHub Actions
Copy link

github-actions bot commented Jul 29, 2024 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit c3511c9

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

❗ 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
@ypriverol
Copy link
Member Author

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
Merged
@ypriverol ypriverol requested a review from daichengxin August 2, 2024 22:46
@jpfeuffer
Copy link
Collaborator

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

@ypriverol
Copy link
Member Author

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
16 checks passed
@jpfeuffer
Copy link
Collaborator

jpfeuffer commented Aug 4, 2024 •
edited
Loading

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
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@daichengxin daichengxin Awaiting requested review from daichengxin

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

Update the pipeline to SDRF validation 0.0.28 Use compressed parquet files for mzml statistics
3 participants
@ypriverol @jpfeuffer @daichengxin