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

Revert nf-test related changes #197

Merged
merged 1 commit into from
Sep 21, 2023
Merged

Revert nf-test related changes #197

merged 1 commit into from
Sep 21, 2023

Conversation

adamrtalbot
Copy link
Contributor

@adamrtalbot adamrtalbot commented Sep 21, 2023 •
edited
Loading

Reverts:
3f31ccc Merge pull request #183 from drpatelh/nf-test
23d2f21 Merge pull request #182 from nf-core/fix/restructured-nf-tests
6cd8d3f Merge pull request #170 from MCMandR/patch-1
47caf0a Merge pull request #176 from sateeshperi/dev
02a44de Merge pull request #174 from sateeshperi/dev
7751398 Merge pull request #172 from nf-core/fix/CI-update-matrix-versions
111b4f5 Merge pull request #171 from davidecarlson/doc_update
50dd8b9 Merge pull request #168 from nf-core/fix/ci-test-template
4d1134a Merge pull request #165 from nf-core/fix/ci-commenter-fixes
c7410ba Merge pull request #164 from nf-core/fix/snap-updates
8abdee5 Merge pull request #163 from nf-core/fix/CI-fixes
f5a8b69 Merge pull request #151 from nf-core/feat/implement-nf-tests
624d420 Merge pull request #161 from ejseqera/fixes

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/fetchngs 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).

@github-actions
Copy link

github-actions bot commented Sep 21, 2023 •
edited
Loading

nf-core lint overall result: Failed ❌

Posted for pipeline commit 4bec299

+| ✅ 140 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   7 tests had warnings |!
-| ❌   7 tests failed       |-

❌ Test failures:

  • nextflow_config - Config variable not found: params.validationShowHiddenParams
  • nextflow_config - Config variable not found: params.validationSchemaIgnoreParams
  • files_unchanged - .github/CONTRIBUTING.md does not match the template
  • files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml does not match the template
  • files_unchanged - assets/nf-core-fetchngs_logo_light.png does not match the template
  • schema_params - Param schema_ignore_params from nextflow config not found in nextflow_schema.json
  • multiqc_config - 'assets/multiqc_config.yml' does not contain a matching 'report_comment'.

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • files_exist - File not found: lib/WorkflowFetchngs.groovy
  • nextflow_config - Config manifest.version should end in dev: 1.10.0
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
  • schema_description - No description provided in schema for parameter: dbgap_key

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/fetchngs/fetchngs/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-09-21 09:31:16

@maxulysse maxulysse changed the title stuff Revert nf-test related changes Sep 21, 2023
@adamrtalbot
Revert dev to release 1.10
4bec299 
This reverts commit 624d420, reversing
changes made to 1b9d187.
maxulysse
maxulysse approved these changes Sep 21, 2023
View reviewed changes
Copy link
Member

@maxulysse maxulysse left a comment

Choose a reason for hiding this comment

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

only linting failing so far, so it's a go for me

@maxulysse
Copy link
Member

Context:
We're reverting the nf-test related changes, so we can TEMPLATE update and have a PR only with nf-test related stuff.
Sorry about the mess, we should have planned things in a better way.

@maxulysse maxulysse merged commit 31fbb80 into dev Sep 21, 2023
9 of 10 checks passed
@maxulysse maxulysse deleted the revert_to_dev_1.10.1 branch October 12, 2023 09:41
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@maxulysse maxulysse maxulysse 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.
2 participants
@adamrtalbot @maxulysse