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

Add end2end part to make it accessible to more users #18

Open
wants to merge 7 commits into
base: dev
Choose a base branch
from
Open

Add end2end part to make it accessible to more users #18

wants to merge 7 commits into from

Conversation

LeonHafner
Copy link
Contributor

I left the file paths in, so you can use the same files on the server @nictru.
We have to discuss somethings in our next meeting (e.g. no apptainer for chipseq, good testing data, non default parameters).

@github-actions GitHub Actions
Copy link

github-actions bot commented Sep 2, 2024 •
edited
Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit cbe5351

+| ✅ 212 tests passed       |+
#| ❔  11 tests were ignored |#
!| ❗  12 tests had warnings |!

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • 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 main.nf: A stub section should mimic the execution of the original module as best as possible
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • 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 awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

  • files_exist - File is ignored: assets/multiqc_config.yml
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • template_strings - Ignoring Jinja template strings in file /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/base.html
  • template_strings - Ignoring Jinja template strings in file /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/configuration.html
  • template_strings - Ignoring Jinja template strings in file /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/macros.html
  • template_strings - Ignoring Jinja template strings in file /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/network.html
  • template_strings - Ignoring Jinja template strings in file /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/snp.html
  • template_strings - Ignoring Jinja template strings in file /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/tf.html
  • template_strings - Ignoring Jinja template strings in file /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/tg.html
  • multiqc_config - multiqc_config

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-11-18 13:13:54

@nictru
Copy link
Collaborator

nictru commented Sep 5, 2024

LGTM so far

@LeonHafner LeonHafner marked this pull request as ready for review November 7, 2024 16:15
@LeonHafner LeonHafner self-assigned this Nov 18, 2024
@LeonHafner LeonHafner requested a review from nictru November 18, 2024 13:19
nictru
nictru requested changes Nov 28, 2024
View reviewed changes
Copy link
Collaborator

@nictru nictru left a comment

Choose a reason for hiding this comment

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

Please add shebang and pipeline versions, so that external pipeline updates can't break our stuff

assets/end_to_end.py

tfactivity_run = f"""
nextflow run \
/nfs/home/students/l.hafner/inspect/tfactivity/dev/main.nf \
Copy link
Collaborator

Choose a reason for hiding this comment

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

Not great

@LeonHafner
Copy link
Contributor Author

#24 should be merged first.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@nictru nictru nictru requested changes

Requested changes must be addressed to merge this pull request.

Assignees

@LeonHafner LeonHafner

Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@LeonHafner @nictru