Skip to content

Command to generate pipeline container config files #3955

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

Open
mirpedrol wants to merge 20 commits into
base: dev
Choose a base branch
from
Open

Command to generate pipeline container config files #3955

Changes from 1 commit
Commits
Show all changes
20 commits
Select commit Hold shift + click to select a range
3e0821a
initial functions to generate pipeline container config files
mirpedrol Dec 2, 2025
f3bd12c
[automated] Update CHANGELOG.md
nf-core-bot Dec 2, 2025
682f140
generate all config files
mirpedrol Dec 2, 2025
54acc5a
regenerate container config files when modules install, remove, update
mirpedrol Dec 2, 2025
b8004aa
pass repo_path
mirpedrol Dec 2, 2025
015daa5
add tests
mirpedrol Dec 2, 2025
b8cf374
less lines
mirpedrol Dec 3, 2025
0954ee6
always update docker amd64
mirpedrol Dec 4, 2025
f5502c9
Update nf_core/pipelines/containers_utils.py
mirpedrol Dec 4, 2025
7d2586d
spaces
mirpedrol Dec 4, 2025
0ab8425
Apply suggestions from code review
mirpedrol Dec 15, 2025
66ef73b
Merge branch 'dev' into pipeline-container-config-builder
mashehu Dec 15, 2025
0eb9323
fix types
mashehu Dec 15, 2025
815102a
update fastqc and multiqc
mirpedrol Dec 16, 2025
426f319
inspect in json format and fix tests
mirpedrol Dec 16, 2025
51eb99b
fix template after updating modules with topics
mirpedrol Dec 16, 2025
d2a797c
update nf-test snapshots
mirpedrol Dec 16, 2025
c3d04f0
add missing commas
mirpedrol Dec 16, 2025
df715e2
simplify functions, thanks @mashehu
mirpedrol Dec 16, 2025
bd98209
Update tests/pipelines/test_container_configs.py
mirpedrol Dec 17, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Prev Previous commit
Next Next commit
[automated] Update CHANGELOG.md
  • Loading branch information
@nf-core-bot @mirpedrol
nf-core-bot authored and mirpedrol committed Dec 2, 2025
commit f3bd12cce584c6989abab8a47b24ac9cf013180f
1 change: 1 addition & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@
- add pre-commit hook to keep uv.lock in sync ([#3933](https://github.com/nf-core/tools/pull/3933))
- Update mcr.microsoft.com/devcontainers/miniconda Docker digest to 2be0f5a ([#3946](https://github.com/nf-core/tools/pull/3946))
- Fix docker errors in test ([#3924](https://github.com/nf-core/tools/pull/3924))
- Add new command to generate pipeline container config files ([#3955](https://github.com/nf-core/tools/pull/3955))

### Template

Expand Down