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Implement wave container commands#3954

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JulianFlesch wants to merge 101 commits intonf-core:devfrom
JulianFlesch:feature/3952-create-waveyml
Draft

Implement wave container commands#3954
JulianFlesch wants to merge 101 commits intonf-core:devfrom
JulianFlesch:feature/3952-create-waveyml

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@JulianFlesch JulianFlesch commented Dec 2, 2025 •
edited by ningyuxin1999
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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
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@mashehu mashehu mentioned this pull request Jan 23, 2026
Draft
mashehu and others added 20 commits January 26, 2026 11:14
@mashehu
add verbose wave output option
6c685fe
@mashehu
fix log parsing
7c9ebb9
@mashehu
try pixi template
7319ba7
@mashehu
fix tests
ca10458
@mashehu
cobmine meta_yml parsing to one shared function
ab425ce
@mashehu
remove obsolete test
4f7c3e5
@mashehu
add container list command
86f6724
@mashehu
fix tests
9ac6064
@mashehu
add force option and fix wave response parsing
ac7dd74
@ningyuxin1999
Merge branch 'dev' into feature/3952-create-waveyml
b80974f
@ningyuxin1999
Revert "Merge branch 'dev' into feature/3952-create-waveyml"
3004d1f 
This reverts commit b80974f, reversing
changes made to ac7dd74.
@ningyuxin1999
Merge branch 'dev' into feature/3952-create-waveyml
290b2c6
@JulianFlesch
Add dummy method
9f7ff2b
@JulianFlesch
Add linting container section of meta.yml as dummy
4548162
@ningyuxin1999
container linting, container section still missing in meta.yml
85e4718
@ningyuxin1999
lint the container var in nfcore_compinent
683e26a
@ningyuxin1999
Merge branch 'dev' into feature/3952-create-waveyml
809723f
@ningyuxin1999
pre-commit fix, mypy error still need to be fixed
278d053
@ningyuxin1999
fix mypy
3735c40
@ningyuxin1999
Merge branch 'dev' into feature/3952-create-waveyml
08a08d0
@mashehu mashehu added this to the 3.6.0 milestone Mar 3, 2026
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