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

Fix genome size #146

Merged
merged 28 commits into from
Sep 25, 2023
Merged

Fix genome size #146

merged 28 commits into from
Sep 25, 2023

Conversation

yumisims
Copy link
Contributor

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
  • 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: Passed ✅ ⚠️

Posted for pipeline commit 580ee1c

+| ✅ 126 tests passed       |+
#| ❔  17 tests were ignored |#
!| ❗   8 tests had warnings |!

❗ 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
  • nextflow_config - Config manifest.version should end in dev: '1.0.0'
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • 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
  • system_exit - System.exit in WorkflowTreeval.groovy: System.exit(1) [line 17]

❔ Tests ignored:

  • files_exist - File is ignored: assets/nf-core-treeval_logo_light.png
  • files_exist - File is ignored: conf/test_full.config
  • files_exist - File is ignored: docs/images/nf-core-treeval_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-treeval_logo_dark.png
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File does not exist: assets/nf-core-treeval_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-treeval_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-treeval_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/treeval/treeval/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-09-25 11:32:17

@DLBPointon DLBPointon self-assigned this Sep 22, 2023
@DLBPointon DLBPointon added the Release 1 Issues required for first release label Sep 22, 2023
@DLBPointon
Copy link
Contributor

Hi @priyanka-surana
This is the previously mentioned hotfix for TreeVal.

It changes one reference in the modules.config file so that the correct file is output for treeval ingestion.

muffato
muffato reviewed Sep 25, 2023
View reviewed changes
docs/usage.md Outdated Show resolved Hide resolved
docs/usage.md Show resolved Hide resolved
@DLBPointon
Copy link
Contributor

I've merged More-docs into this branch

muffato
muffato approved these changes Sep 25, 2023
View reviewed changes
Copy link
Member

@muffato muffato left a comment

Choose a reason for hiding this comment

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

The only addition of this PR to #145 is the change in conf/modules.config

@DLBPointon DLBPointon merged commit 28309b7 into dev Sep 25, 2023
@DLBPointon DLBPointon deleted the fix_genome_size branch September 25, 2023 13:09
@muffato muffato added this to the Release 1 milestone Sep 25, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@DLBPointon DLBPointon DLBPointon left review comments

@muffato muffato muffato approved these changes

@priyanka-surana priyanka-surana Awaiting requested review from priyanka-surana

Assignees

@DLBPointon DLBPointon

Labels
Release 1 Issues required for first release
Projects
None yet
Milestone
Release 1
Development

Successfully merging this pull request may close these issues.
3 participants
@yumisims @DLBPointon @muffato