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

[WIP] Trying to set up basic workflow #2

Closed
wants to merge 34 commits into from
Closed

[WIP] Trying to set up basic workflow #2

wants to merge 34 commits into from

Conversation

WackerO
Copy link
Collaborator

@WackerO WackerO commented Oct 24, 2022

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).

ggabernet
ggabernet reviewed Oct 25, 2022
View reviewed changes
Copy link
Member

@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.

Here some comments already, just noticeably, the testdata folder should not be there as the test data for pipelines should be hosted in the github.com/nf-core/test-datasets repo. If it's already available in the modules branch you can use that one. Also the modules tests are not included in the pipeline repo, these are only in the nf-core/modules repo.

.github/ISSUE_TEMPLATE/feature_request.yml Outdated Show resolved Hide resolved
testdata/Sample_preparations.tsv Outdated Show resolved Hide resolved
testdata/contrast_meta.csv Outdated Show resolved Hide resolved
tests/config/pytest_modules.yml Outdated Show resolved Hide resolved
tests/config/test_data.config Outdated Show resolved Hide resolved
workflows/differentialabundance.nf Outdated Show resolved Hide resolved
workflows/differentialabundance.nf Outdated Show resolved Hide resolved
@pinin4fjords
Copy link
Member

Any chance of splitting this PR into smaller ones with specific objective to facilitate review? The interesting workflow changes are getting a bit lost among everything else.

@WackerO
Copy link
Collaborator Author

WackerO commented Oct 25, 2022

Any chance of splitting this PR into smaller ones with specific objective to facilitate review? The interesting workflow changes are getting a bit lost among everything else.

hmm it seems like something went wrong with the pipeline creation from the template then here? It might be best to create it again from scratch, otherwise you might have this issue again for every template update

Yeah, the general changes do clutter the central changes indeed...I'll see tomorrow if I actually have to reconstruct the pipeline because of the differentialabundance/differentialabundance problem that Gisela noted, then I'll do separate PRs for the bla stuff and the actual workflow changes

@WackerO WackerO changed the base branch from dev to master October 28, 2022 07:56
@WackerO WackerO changed the base branch from master to dev October 28, 2022 07:56
@WackerO
Copy link
Collaborator Author

WackerO commented Nov 2, 2022

@nf-core-bot fix linting

@github-actions
Copy link

github-actions bot commented Nov 2, 2022 •
edited
Loading

nf-core lint overall result: Failed ❌

Posted for pipeline commit c56359c

+| ✅ 152 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗  23 tests had warnings |!
-| ❌   3 tests failed       |-

❌ Test failures:

  • schema_params - Param input from nextflow config not found in nextflow_schema.json
  • schema_params - Default value for param samplesheet invalid: Not in pipeline parameters. Check nextflow.config.
  • schema_params - Default value for param multiqc_title invalid: Not in pipeline parameters. Check nextflow.config.

❗ Test warnings:

  • pipeline_todos - TODO string in README.md: Add full-sized test dataset and amend the paragraph below if applicable
  • pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
  • 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
  • pipeline_todos - TODO string in test.yml: #Please run the following command to build this file:
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in test_rnaseq_featurecounts.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in test_rnaseq_featurecounts.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • pipeline_todos - TODO string in meta.yml: #Add a description of the module and list keywords
  • pipeline_todos - TODO string in meta.yml: #Add a description and other details for the software below
  • pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as input
  • pipeline_todos - TODO string in meta.yml: #Delete / customise this example input
  • pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as output
  • pipeline_todos - TODO string in meta.yml: #Delete / customise this example output
  • schema_lint - Parameter input not found in schema
  • schema_params - Schema param samplesheet not found from nextflow config
  • schema_params - Schema param multiqc_title not found from nextflow config

❔ Tests ignored:

  • 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: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.6
  • Run at 2022-11-28 13:57:00

@WackerO
Copy link
Collaborator Author

WackerO commented Nov 3, 2022

@nf-core-bot fix linting

@WackerO WackerO added WIP This issue is already being worked on and removed WIP This issue is already being worked on labels Nov 28, 2022
@WackerO WackerO mentioned this pull request Nov 30, 2022
Closed
@WackerO WackerO closed this Feb 15, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@ggabernet ggabernet ggabernet left review comments

@pinin4fjords pinin4fjords pinin4fjords left review comments

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
4 participants
@WackerO @pinin4fjords @ggabernet @nf-core-bot