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Implement wave container commands #3954

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Implement wave container commands #3954

JulianFlesch wants to merge 90 commits into from
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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
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mashehu commented Jan 17, 2026

Added the meta_yml sorting now. I also switched the default value of --await to true, because it wouldn't get the singularity https links by default.

@mashehu mashehu force-pushed the feature/3952-create-waveyml branch from 1de5380 to b92491a Compare January 21, 2026 15:45
@mashehu mashehu mentioned this pull request Jan 23, 2026
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