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Implement wave container commands#3954

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JulianFlesch wants to merge 246 commits intonf-core:devfrom
JulianFlesch:feature/3952-create-waveyml
Draft

Implement wave container commands#3954
JulianFlesch wants to merge 246 commits intonf-core:devfrom
JulianFlesch:feature/3952-create-waveyml

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@JulianFlesch JulianFlesch commented Dec 2, 2025 •
edited by mashehu
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Closes #3952

  • nf-core modules containers create [module-name]
  • nf-core modules containers conda-lock [module-name]
  • nf-core modules containers lint [module-name]
  • nf-core modules containers list [module-name]

@ningyuxin1999 ningyuxin1999 self-assigned this Dec 2, 2025
@JulianFlesch JulianFlesch changed the title switch pre-commit to prek for development Implement wave container commands Dec 2, 2025
ningyuxin1999 and others added 20 commits December 2, 2025 13:30
@ningyuxin1999
added architecture
6b73c3c
@ningyuxin1999
Merge branch 'dev' into feature/3952-create-waveyml
5819387
@ningyuxin1999
wire commands with functions
e689754
@ningyuxin1999
Merge branch 'feature/3952-create-waveyml' of https://github.com/Juli…
c8873db 
…anFlesch/nf-core-tools into feature/3952-create-waveyml
@ningyuxin1999
containers obj
8328f6f
@ningyuxin1999
Merge branch 'dev' into feature/3952-create-waveyml
6fba8ae
@JulianFlesch
Update resolve module_dir. Change to using ValueError
78358ae
@JulianFlesch
Add TODOs
4493cad
@JulianFlesch
WIP: add container listing
1915c15
@JulianFlesch
Move container constants to global utils.
109d0b8
@JulianFlesch
Use constants from global utils. Change list_containers to return lis…
e723d5b 
…t instead of printing. simplify checks
@ningyuxin1999
add dry-run to the containers create, fixed the uitls import and modu…
f44757b 
…le path
@JulianFlesch
Add contextmanager that extends set_wd but changes into a tempdir
7c369a4
@JulianFlesch
Add extracting container string from a module main.nf
81ddaf8
@JulianFlesch
Rename method to match field name
882ed67
@JulianFlesch
Print container info as richt table
aa9fa01
@JulianFlesch
Merge branch 'feature/3952-create-waveyml' of github.com:JulianFlesch…
3e119a4 
…/nf-core-tools into feature/3952-create-waveyml
@JulianFlesch
Move calling wave to ModuleContainers class. Finish create method and…
11228d4 
… add dry_run arg
@JulianFlesch
Fix output encoding
c08a6dd
@JulianFlesch
Remove comment
c6e8360
mashehu
mashehu reviewed Dec 4, 2025
View reviewed changes
Comment thread nf_core/components/nfcore_component.py
ningyuxin1999 and others added 25 commits March 31, 2026 10:57
@ningyuxin1999 @mashehu
output the summary of modules lint
181b394
@JulianFlesch @mashehu
Wrap platform strings into custom class to treat / and _ equivalently
ee47750
@JulianFlesch @mashehu
Add explicit conversion to slash format where needed e.g. docker or w…
d6145d7 
…ave commands
@JulianFlesch @mashehu
Remove conversion methods
8354726
@JulianFlesch @mashehu
Adress container platform spelling ambiguities
3afe202
@ningyuxin1999 @mashehu
fix tests
1d528d0
@ningyuxin1999 @mashehu
move skip nf test to meta_yml.py, skip checks by labels.
c69aad0
@mashehu
add type hint and docstring
4750554
@mashehu
switch to "linux/a{rm,md}64" (slash-version) to avoid all the tooling
b92bbda
@mashehu
test with more realistic IDs (without platform info)
10de7e1
@mashehu
update uv.lock
f15d68c
@mashehu
switch container linting from fail to warn for now
c5cb5bd
@mashehu
remove containers lint command, it is anyway part of modules lint
0093c26
@mashehu
switch back to scan_id and build_id to keep in sync with schema
6ad3b47
@mashehu
replace progressbar with spinner
aeb517f
@mashehu
deprecate old container checks
acebcf0
@mashehu
move bioconda version checking to environment.yml checks
dad1d79
@mashehu
remove linting for conda-lock file urls
2c5dac3
@mashehu
use key variables in test file to keep them in sync
3d42c45
@mashehu
simplify module parsing code
43ca5dd
@mashehu
add local module container tests
bacd18e
@mashehu
add per container spinner
3bfcdc3
@mashehu
fix meta yaml linting test
b484b8b
@mashehu
fix linting error
50e5249
@mashehu
fix jinja variable in template
1efe0f5
@mashehu mashehu force-pushed the feature/3952-create-waveyml branch from 693bb90 to 1efe0f5 Compare March 31, 2026 08:59
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@mashehu mashehu mashehu approved these changes

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Status: In progress

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@JulianFlesch @mashehu @ningyuxin1999 @nf-core-bot @andresferben