+
Skip to content

update module commands with new format #983

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.

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

Merged
merged 5 commits into from
Apr 9, 2021

Conversation

KevinMenden
Copy link
Contributor

This updates the module commands create and create-test-yml with the new module format for the test.yml

Instead of tool_subtool the tag will now be tool/subtool (see here: nf-core/modules#389)

Still need to update the lint command to look for the correct tags if we decided to go only for these tags instead of having things like "my_tool_single_end" etc.

@codecov
Copy link

codecov bot commented Mar 29, 2021

Codecov Report

Merging #983 (7d23409) into dev (a3214aa) will not change coverage.
The diff coverage is 0.00%.

Impacted file tree graph

@@           Coverage Diff           @@
##              dev     #983   +/-   ##
=======================================
  Coverage   69.23%   69.23%           
=======================================
  Files          34       34           
  Lines        4261     4261           
=======================================
  Hits         2950     2950           
  Misses       1311     1311           
Impacted Files Coverage Δ
nf_core/modules/create.py 59.57% <0.00%> (ø)
nf_core/modules/lint.py 62.55% <ø> (ø)
nf_core/modules/test_yml_builder.py 16.04% <0.00%> (ø)

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update a3214aa...7d23409. Read the comment docs.

@ewels ewels added the WIP Work in progress label Mar 29, 2021
@KevinMenden KevinMenden changed the title update module commans with new format update module commands with new format Mar 30, 2021
@KevinMenden KevinMenden marked this pull request as ready for review April 8, 2021 08:10
@KevinMenden KevinMenden added ready-for-review and removed WIP Work in progress labels Apr 8, 2021
@drpatelh
Copy link
Member

drpatelh commented Apr 8, 2021

Thanks @KevinMenden ! Need to change the format of the module in pytest_software.yml too when creating modules.

@KevinMenden
Copy link
Contributor Author

Right, thanks @drpatelh ! Changed that, now it should work.

@KevinMenden
Copy link
Contributor Author

pytest_software.yml now looks like this:

tool/subtool:
  - software/tool/subtool/**
  - tests/software/tool/subtool/**

Copy link
Member

@drpatelh drpatelh left a comment

Choose a reason for hiding this comment

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

LGTM!

@drpatelh drpatelh merged commit 35d7685 into nf-core:dev Apr 9, 2021
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

3 participants
点击 这是indexloc提供的php浏览器服务,不要输入任何密码和下载