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

Interactive plots (6) #151

Merged
merged 38 commits into from
Oct 20, 2022
Merged

Interactive plots (6) #151

merged 38 commits into from
Oct 20, 2022

Conversation

WackerO
Copy link
Collaborator

@WackerO WackerO commented Aug 11, 2022 •
edited
Loading

PCA plots and heatmaps are now interactive (no issue, this was a point in trello); also adds a sessioninfo to the report and closes #55. Additionally, volcano and gost plots are now cleaned up a bit, closes #160

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/rnadeseq 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

This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @WackerO,

It looks like this pull-request is has been made against the WackerO/rnadeseq master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the WackerO/rnadeseq dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@WackerO WackerO changed the title Interactive PCA plots Interactive PCA plots (6) Aug 11, 2022
@WackerO WackerO requested a review from ggabernet August 11, 2022 07:07
@github-actions
Copy link

github-actions bot commented Aug 11, 2022 •
edited
Loading

nf-core lint overall result: Failed ❌

Posted for pipeline commit 21e0f21

+| ✅ 116 tests passed       |+
#| ❔  26 tests were ignored |#
!| ❗   9 tests had warnings |!
-| ❌   4 tests failed       |-

❌ Test failures:

  • files_exist - File not found: .prettierignore
  • files_unchanged - lib/NfcoreTemplate.groovy does not match the template
  • actions_ci - '.github/workflows/ci.yml' does not check minimum NF version
  • multiqc_config - 'assets/multiqc_config.yml' does not contain a matching 'report_comment'.

❗ Test warnings:

  • files_exist - File not found: pyproject.toml
  • readme - README did not have a Nextflow minimum version badge.
  • readme - README did not have a Nextflow minimum version mentioned in Quick Start section.
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • pipeline_todos - TODO string in rnadeseq.nf: Add all file path parameters for the pipeline to the list below
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • schema_lint - Parameter input not found in schema

❔ Tests ignored:

  • files_exist - File is ignored: assets/nf-core-qbic-pipelines/rnadeseq_logo_light.png
  • files_exist - File is ignored: conf/test_full.config
  • files_exist - File is ignored: docs/images/nf-core-qbic-pipelines/rnadeseq_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-qbic-pipelines/rnadeseq_logo_dark.png
  • files_exist - File is ignored: bin/markdown_to_html.r
  • files_exist - File is ignored: .github/workflows/push_dockerhub.yml
  • files_exist - File is ignored: assets/multiqc_config.yaml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: lib/WorkflowQbic-pipelines/rnadeseq.groovy
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • nextflow_config - Config variable ignored: params.input
  • 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/ISSUE_TEMPLATE/config.yml
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/feature_request.yml
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File ignored due to lint config: docs/README.md
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml

✅ Tests passed:

Run details

  • nf-core/tools version 2.5.1
  • Run at 2022-09-27 12:30:08

@WackerO WackerO changed the title Interactive PCA plots (6) Interactive plots (6) Aug 12, 2022
@WackerO WackerO changed the base branch from master to dev September 6, 2022 12:25
@WackerO WackerO marked this pull request as ready for review September 6, 2022 13:25
ggabernet
ggabernet reviewed Sep 14, 2022
View reviewed changes
assets/RNAseq_report.Rmd Show resolved Hide resolved
assets/RNAseq_report.Rmd Show resolved Hide resolved
@WackerO
fixed pathway plot limits
1698a32
@WackerO
excluded batch from output, added samplename to interactive PCA plots,
9943a3e 
improved plot layout
@WackerO
Removed batch comparison files from batch test yml, changed file names
f5d8071 
of test_contrast_matrix.yml (files don't contain "condition_" in their
names anymore)
@WackerO
Changed some file names in test yml
21e0f21
@WackerO
Updated file paths
fd5b01c
@WackerO
just added a space, this commit is to try and run the github tests which
83c87cc 
previously did not activate
@WackerO
Updated batch 5sums
0d47b66
@WackerO
Trying again with different paths; I won't update the 5sums for now as
3ff9e12 
they are unstable during container changes
@WackerO
Fixed some more paths
eb413ce
@WackerO
updated changelog
c81b236
@WackerO
fixed more typos in paths
060f457
@WackerO
hopefully last typo fix
ec7b6f1
@WackerO
one more path corrected, also updated 5sum
c00cc38
@WackerO
Copy link
Collaborator Author

WackerO commented Oct 6, 2022

@ggabernet this is ready for another review :) the batch run is again unstable in its 5sums because I changed the container; will do a follow-up mini PR to check the sums

ggabernet
ggabernet approved these changes Oct 20, 2022
View reviewed changes
Copy link
Collaborator

@ggabernet ggabernet left a comment

Choose a reason for hiding this comment

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

Looks good to me!

assets/RNAseq_report.Rmd Show resolved Hide resolved
@WackerO WackerO merged commit ceb515d into qbic-pipelines:dev Oct 20, 2022
@WackerO WackerO deleted the pca branch October 20, 2022 10:24
@WackerO WackerO mentioned this pull request Oct 25, 2022
Closed
@WackerO WackerO mentioned this pull request Nov 29, 2022
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@ggabernet ggabernet ggabernet 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.

None yet
2 participants
@WackerO @ggabernet