Thanks to visit codestin.com
Credit goes to github.com

Skip to content

Rewrote nf-core launch #591

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
Merged
ewels merged 3 commits into from
Mar 25, 2020
Merged

Rewrote nf-core launch #591

ewels merged 3 commits into from
Mar 25, 2020

Conversation

@ewels
Copy link
Member

@ewels ewels commented Mar 20, 2020 •
edited
Loading

Rewrote nf-core launch to use the new JSON Schema pipeline parameters. Removed a lot of old code. Also fixed up some of the parameter typing in nf-core schema build

Still to do:

  • Fix (? for help) in booleans
  • Make -a flag do what it is supposed to do
  • Use defaults from nextflow config instead of schema? (warn if different from schema)
  • When pulling, get latest release or if no release then default branch.
  • Test with non-nf-core pipelines
  • Description and help text for groups
  • Check python tests
  • Check that importing a params file at launch time works
  • Update documentation
  • Update changelog

For a future PR:

  • Link to the website for using a GUI to prepare parameters, instead of the CLI (if desired)

@ewels ewels added the WIP Work in progress label Mar 20, 2020
@ewels ewels requested a review from a team March 20, 2020 20:21
@codecov
Copy link

codecov bot commented Mar 20, 2020 •
edited
Loading

Codecov Report

Merging #591 into dev will decrease coverage by 1.54%.
The diff coverage is 8.24%.

Impacted file tree graph

@@            Coverage Diff             @@
##              dev     #591      +/-   ##
==========================================
- Coverage   68.10%   66.55%   -1.55%     
==========================================
  Files          13       11       -2     
  Lines        2091     1848     -243     
==========================================
- Hits         1424     1230     -194     
+ Misses        667      618      -49
Impacted Files Coverage Δ
nf_core/launch.py 0.00% <0.00%> (-14.11%) ⬇️
nf_core/list.py 76.57% <15.00%> (-6.10%) ⬇️
nf_core/schema.py 73.72% <70.58%> (-0.16%) ⬇️
nf_core/__init__.py 100.00% <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 84a8399...8d4d503. Read the comment docs.

@ewels ewels removed the request for review from a team March 21, 2020 06:02
@drpatelh drpatelh removed the WIP Work in progress label Mar 25, 2020
@ewels ewels mentioned this pull request Mar 25, 2020
Closed
11 tasks
@ewels ewels merged commit 8142260 into nf-core:dev Mar 25, 2020
@ewels ewels deleted the stand-alone-schema branch July 9, 2020 14:05
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@drpatelh drpatelh drpatelh 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.

2 participants

@ewels @drpatelh