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

Bugfix/aws staging #9

Merged
merged 4 commits into from
Feb 23, 2024
Merged

Bugfix/aws staging #9

merged 4 commits into from
Feb 23, 2024

Conversation

jspaezp
Copy link
Collaborator

@jspaezp jspaezp commented Feb 7, 2024 •
edited
Loading

This PR does a couple of things ...

  1. Fixes bin/diann_convert.py, it was failing when no ambiguous protein groups are present. (some minor cleanup and auto formatting...)
  2. bin/mzml_statistics.py adds better error messages and prevents a general exception handle
  3. workflows/dia.nf fixes the workflow ... even though the last version was only searching a subset of the files, all of them were still being staged, this changes stages only the needed ones.
  4. workflows/quantms.nf (untested ..) fixes an issue where no slack messages were sent when the pipeline failed.

@github-actions GitHub Actions
Copy link

github-actions bot commented Feb 7, 2024

Python linting (black) is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:

  • Install black: pip install black
  • Fix formatting errors in your pipeline: black .

Once you push these changes the test should pass, and you can hide this comment 👍

We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!

@github-actions GitHub Actions
Copy link

github-actions bot commented Feb 7, 2024 •
edited
Loading

nf-core lint overall result: Failed ❌

Posted for pipeline commit 86475cc

+| ✅ 259 tests passed       |+
#| ❔   4 tests were ignored |#
-| ❌  20 tests failed       |-

❌ Test failures:

  • files_exist - File must be removed: lib/nfcore_external_java_deps.jar
  • nextflow_config - Config default value incorrect: params.outdir is set as ./results in nextflow_schema.json but is null in nextflow.config.
  • nextflow_config - Config default value incorrect: params.acquisition_method is set as dda in nextflow_schema.json but is null in nextflow.config.
  • nextflow_config - Config default value incorrect: params.instrument is set as high_res in nextflow_schema.json but is null in nextflow.config.
  • nextflow_config - Config default value incorrect: params.run_fdr_cutoff is set as 0.01 in nextflow_schema.json but is 0.10 in nextflow.config.
  • nextflow_config - Config default value incorrect: params.feature_with_id_min_score is set as 0.0 in nextflow_schema.json but is 0.10 in nextflow.config.
  • nextflow_config - Config default value incorrect: params.feature_without_id_min_score is set as 0.0 in nextflow_schema.json but is 0.75 in nextflow.config.
  • nextflow_config - Config default value incorrect: params.lfq_intensity_threshold is set as 10000.0 in nextflow_schema.json but is 1000 in nextflow.config.
  • nextflow_config - Config default value incorrect: params.scan_window is set as 7 in nextflow_schema.json but is 8 in nextflow.config.
  • nextflow_config - Config default value incorrect: params.max_memory is set as 128.GB in nextflow_schema.json but is 128 GB in nextflow.config.
  • nextflow_config - Config default value incorrect: params.max_time is set as 240.h in nextflow_schema.json but is 10d in nextflow.config.
  • files_unchanged - .github/workflows/branch.yml does not match the template
  • files_unchanged - .github/workflows/linting_comment.yml does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • files_unchanged - assets/email_template.html does not match the template
  • files_unchanged - assets/email_template.txt does not match the template
  • files_unchanged - assets/nf-core-quantms_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-quantms_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-quantms_logo_dark.png does not match the template
  • files_unchanged - pyproject.toml does not match the template

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-09 20:49:59

@jspaezp jspaezp requested review from wfondrie and cia23 February 9, 2024 21:06
wfondrie
wfondrie approved these changes Feb 9, 2024
View reviewed changes
Copy link
Member

@wfondrie wfondrie left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

LGTM - I think this should fix it. However, I don't think this will be able to be merged into the nf-core pipeline with the notification change. I suspect that that change will need to be made against the nf-core template instead, so it can trickle down to all pipelines.

cia23
cia23 approved these changes Feb 12, 2024
View reviewed changes
Copy link

@cia23 cia23 left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

LGTM

@jspaezp jspaezp marked this pull request as ready for review February 23, 2024 16:10
@jspaezp jspaezp merged commit 9f4cd5b into dev Feb 23, 2024
10 of 17 checks passed
@jspaezp jspaezp deleted the bugfix/aws_staging branch February 23, 2024 16:11
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@wfondrie wfondrie wfondrie approved these changes

@cia23 cia23 cia23 approved these changes

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

Successfully merging this pull request may close these issues.
3 participants
@jspaezp @wfondrie @cia23