Implement wave container commands#3954

Draft

JulianFlesch wants to merge 172 commits into

nf-core:devfrom

JulianFlesch:feature/3952-create-waveyml

Commits on May 8, 2026

WIP: Start working on wave commands: Add command dummies.

JulianFlesch
authored and
mashehu
committed
added architecture

ningyuxin1999
authored and
mashehu
committed
wire commands with functions

ningyuxin1999
authored and
mashehu
committed
containers obj

ningyuxin1999
authored and
mashehu
committed
Update resolve module_dir. Change to using ValueError

JulianFlesch
authored and
mashehu
committed
Add TODOs

JulianFlesch
authored and
mashehu
committed
WIP: add container listing

JulianFlesch
authored and
mashehu
committed
Move container constants to global utils.

JulianFlesch
authored and
mashehu
committed
Use constants from global utils. Change list_containers to return list instead of printing. simplify checks

JulianFlesch
authored and
mashehu
committed
Add contextmanager that extends set_wd but changes into a tempdir

JulianFlesch
authored and
mashehu
committed
Add extracting container string from a module main.nf

JulianFlesch
authored and
mashehu
committed
Rename method to match field name

JulianFlesch
authored and
mashehu
committed
Print container info as richt table

JulianFlesch
authored and
mashehu
committed
add dry-run to the containers create, fixed the uitls import and module path

ningyuxin1999
authored and
mashehu
committed
Move calling wave to ModuleContainers class. Finish create method and add dry_run arg

JulianFlesch
authored and
mashehu
committed
Fix output encoding

JulianFlesch
authored and
mashehu
committed
Remove comment

JulianFlesch
authored and
mashehu
committed
Add TODOs

JulianFlesch
authored and
mashehu
committed
buildid and scanid saved to the dict

ningyuxin1999
authored and
mashehu
committed
meta yaml

ningyuxin1999
authored and
mashehu
committed
Update calling wave command to get buildId/scanId. Only add to outpu if they exist.

JulianFlesch
authored and
mashehu
committed
Simplify create method

JulianFlesch
authored and
mashehu
committed
Refactor to reuse key constants.

JulianFlesch
authored and
mashehu
committed
Add conda-lock information to containers dict

JulianFlesch
authored and
mashehu
committed
Fix space in url

JulianFlesch
authored and
mashehu
committed
Implement conda lock functions. Do not fail in containers_from_meta if containers section missing

JulianFlesch
authored and
mashehu
committed
Simplify class

JulianFlesch
authored and
mashehu
committed
Implement updating meta - WIP: sorting

JulianFlesch
authored and
mashehu
committed
Fix ModuleContainers initialisation

JulianFlesch
authored and
mashehu
committed
Fix expected meta.yml path

JulianFlesch
authored and
mashehu
committed
Update containers in meta.yml - WIP: sorting

JulianFlesch
authored and
mashehu
committed
update container from meta method

JulianFlesch
authored and
mashehu
committed
Review: Rename conda lock methods

JulianFlesch
authored and
mashehu
committed
Fix typo

JulianFlesch
authored and
mashehu
committed
Review command: Remove dry_run flag for module container creation#

JulianFlesch
authored and
mashehu
committed
remove unnecessary string casting

JulianFlesch
authored and
mashehu
committed
Review comment: Remove extra loop for conda-lock files

JulianFlesch
authored and
mashehu
committed
Make wave container requests run concurrently

JulianFlesch
authored and
mashehu
committed
fix gathering concurrent results

JulianFlesch
authored and
mashehu
committed
fix building conda section

JulianFlesch
authored and
mashehu
committed
Remove threads option.

JulianFlesch
authored and
mashehu
committed
fix variable name typo

JulianFlesch
authored and
mashehu
committed
Add wave inspect request to obtain https-urls for singularity images

JulianFlesch
authored and
mashehu
committed
Only attempt retrieving image https-url if the image build is being awaited

JulianFlesch
authored and
mashehu
committed
change to reading from uri from specific layer metadata in manifest in favor of attempting to build it.

JulianFlesch
authored and
mashehu
committed
Remove unused constants

JulianFlesch
authored and
mashehu
committed
simplify extracting uri

JulianFlesch
authored and
mashehu
committed
Change to building url as suggested by ewels in https://github.com/nf-core/modules/issues/6694#issuecomment-2376197663

JulianFlesch
authored and
mashehu
committed
Remove todo

JulianFlesch
authored and
mashehu
committed
make sort_meta_yml a proper method
mashehu
committed
rename metayaml_path to meta_yml_path
mashehu
committed
reuse NFCoreComponent functionality
mashehu
committed
add meta.yml sorting
mashehu
committed
switch to ruamel_yaml and run prettier on dumped file
mashehu
committed
default await to true for container build to always get all info
mashehu
committed
handle empty module input and harmonize prompt function
mashehu
committed
add aliases
mashehu
committed
handle also local modules
mashehu
committed
add conda lock file download functionality
mashehu
committed
differentiate behaviour between pipelines modules (runs on local modules) vs modules repo
mashehu
committed
add warning when wave build failed
mashehu
committed
tests for the module container, lint still missing

ningyuxin1999
authored and
mashehu
committed
run prek
mashehu
committed
handle raised runtime error
mashehu
committed
check for tower_access_token
mashehu
committed
fix tests
mashehu
committed
add progress bar
mashehu
committed
clean up stale conda-lock files
mashehu
committed
also update the container string in the main.nf with the new image
mashehu
committed
add verbose wave output option
mashehu
committed
fix log parsing
mashehu
committed
try pixi template
mashehu
committed
fix tests
mashehu
committed
cobmine meta_yml parsing to one shared function
mashehu
committed
remove obsolete test
mashehu
committed
add container list command
mashehu
committed
fix tests
mashehu
committed
add force option and fix wave response parsing
mashehu
committed
bump to 3.6.0dev
mashehu
committed
Add dummy method

JulianFlesch
authored and
mashehu
committed
Add linting container section of meta.yml as dummy

JulianFlesch
authored and
mashehu
committed
container linting, container section still missing in meta.yml

ningyuxin1999
authored and
mashehu
committed
lint the container var in nfcore_compinent

ningyuxin1999
authored and
mashehu
committed
pre-commit fix, mypy error still need to be fixed

ningyuxin1999
authored and
mashehu
committed
fix mypy

ningyuxin1999
authored and
mashehu
committed
Add module_containers dummy

JulianFlesch
authored and
mashehu
committed
Restructure linting logic into parts. Add ToDos

JulianFlesch
authored and
mashehu
committed
Add nextflow_inspect to utils.

JulianFlesch
authored and
mashehu
committed
Change return type of nextflow_inspect

JulianFlesch
authored and
mashehu
committed
Don't ever return None from nextflow_inspect

JulianFlesch
authored and
mashehu
committed
WIP module containers

JulianFlesch
authored and
mashehu
committed
Lint mainnf container done

JulianFlesch
authored and
mashehu
committed
Fix command creation and path for nextflow inspect

JulianFlesch
authored and
mashehu
committed
Fix access to nextflow inspect output. Refactor to use try-except clause over nexted get()

JulianFlesch
authored and
mashehu
committed
output the summary of modules lint

ningyuxin1999
authored and
mashehu
committed
Wrap platform strings into custom class to treat / and _ equivalently

JulianFlesch
authored and
mashehu
committed
Add explicit conversion to slash format where needed e.g. docker or wave commands

JulianFlesch
authored and
mashehu
committed
Remove conversion methods

JulianFlesch
authored and
mashehu
committed
Adress container platform spelling ambiguities

JulianFlesch
authored and
mashehu
committed
fix tests

ningyuxin1999
authored and
mashehu
committed
move skip nf test to meta_yml.py, skip checks by labels.

ningyuxin1999
authored and
mashehu
committed
add type hint and docstring
mashehu
committed
switch to "linux/a{rm,md}64" (slash-version) to avoid all the tooling
mashehu
committed
test with more realistic IDs (without platform info)
mashehu
committed
switch container linting from fail to warn for now
mashehu
committed
remove containers lint command, it is anyway part of `modules lint`
mashehu
committed
switch back to scan_id and build_id to keep in sync with schema
mashehu
committed
replace progressbar with spinner
mashehu
committed
deprecate old container checks
mashehu
committed
move bioconda version checking to environment.yml checks
mashehu
committed
remove linting for conda-lock file urls
mashehu
committed
use key variables in test file to keep them in sync
mashehu
committed
simplify module parsing code
mashehu
committed
add local module container tests
mashehu
committed
add per container spinner
mashehu
committed
fix meta yaml linting test
mashehu
committed
fix linting error
mashehu
committed
disable warning count until we migrate gitlab modules to containers
mashehu
committed
show completed checkmarks for finished spinners
mashehu
committed
update to new container naming with included registry
mashehu
committed
fix linting
mashehu
committed

Commits

Commits on May 8, 2026

Commits on May 21, 2026

Commits on May 22, 2026