Implement wave container commands by JulianFlesch · Pull Request #3954 · nf-core/tools

Commits on Dec 2, 2025

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Merge branch 'dev' into feature/3952-create-waveyml
JulianFlesch
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Commits on Dec 15, 2025

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also update the container string in the main.nf with the new image
mashehu
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Commits on Jan 26, 2026

add verbose wave output option
mashehu
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Merge branch 'dev' into feature/3952-create-waveyml
ningyuxin1999
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Commits on Feb 12, 2026

Commits on Feb 17, 2026

container linting, container section still missing in meta.yml
ningyuxin1999
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Merge branch 'dev' into feature/3952-create-waveyml
ningyuxin1999
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Commits on Mar 11, 2026

Commits on Mar 12, 2026

Commits on Mar 31, 2026

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

JulianFlesch
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mashehu
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[automated] Update CHANGELOG.md

nf-core-bot
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mashehu
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added architecture

ningyuxin1999
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mashehu
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wire commands with functions

ningyuxin1999
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containers obj

ningyuxin1999
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mashehu
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Update resolve module_dir. Change to using ValueError

JulianFlesch
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Add TODOs

JulianFlesch
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WIP: add container listing

JulianFlesch
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Move container constants to global utils.

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

JulianFlesch
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Add contextmanager that extends set_wd but changes into a tempdir

JulianFlesch
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Add extracting container string from a module main.nf

JulianFlesch
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Rename method to match field name

JulianFlesch
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Print container info as richt table

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

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

JulianFlesch
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mashehu
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Fix output encoding

JulianFlesch
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Remove comment

JulianFlesch
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Add TODOs

JulianFlesch
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buildid and scanid saved to the dict

ningyuxin1999
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meta yaml

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

JulianFlesch
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Simplify create method

JulianFlesch
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Refactor to reuse key constants.

JulianFlesch
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Add conda-lock information to containers dict

JulianFlesch
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Fix space in url

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Implement conda lock functions. Do not fail in containers_from_meta if containers section missing

JulianFlesch
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Simplify class

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Implement updating meta - WIP: sorting

JulianFlesch
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Fix ModuleContainers initialisation

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Fix expected meta.yml path

JulianFlesch
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Update containers in meta.yml - WIP: sorting

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update container from meta method

JulianFlesch
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Review: Rename conda lock methods

JulianFlesch
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Fix typo

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Review command: Remove dry_run flag for module container creation#

JulianFlesch
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remove unnecessary string casting

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Review comment: Remove extra loop for conda-lock files

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Make wave container requests run concurrently

JulianFlesch
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fix gathering concurrent results

JulianFlesch
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fix building conda section

JulianFlesch
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Remove threads option.

JulianFlesch
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fix variable name typo

JulianFlesch
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Add wave inspect request to obtain https-urls for singularity images

JulianFlesch
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Only attempt retrieving image https-url if the image build is being awaited

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change to reading from uri from specific layer metadata in manifest in favor of attempting to build it.

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Remove unused constants

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simplify extracting uri

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

JulianFlesch
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Remove todo

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

ningyuxin1999
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mashehu
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run prek
mashehu
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handle raised runtime error
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check for tower_access_token
mashehu
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fix tests
mashehu
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add progress bar
mashehu
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clean up stale conda-lock files
mashehu
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also update the container string in the main.nf with the new image
mashehu
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add verbose wave output option
mashehu
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fix log parsing
mashehu
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try pixi template
mashehu
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fix tests
mashehu
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cobmine meta_yml parsing to one shared function
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remove obsolete test
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add container list command
mashehu
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fix tests
mashehu
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add force option and fix wave response parsing
mashehu
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Simplify coverage reporting in pytest.yml (#3934)
mashehu
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Update pre-commit hook astral-sh/ruff-pre-commit to v0.14.7 (#3943)

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Update python:3.14-slim Docker digest to 119fd5b (#3910)

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Subworkflow lint bugfixes (#3968)

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bump to 3.6.0dev
mashehu
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Add dummy method

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

JulianFlesch
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container linting, container section still missing in meta.yml

ningyuxin1999
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lint the container var in nfcore_compinent

ningyuxin1999
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pre-commit fix, mypy error still need to be fixed

ningyuxin1999
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fix mypy

ningyuxin1999
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Add module_containers dummy

JulianFlesch
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Restructure linting logic into parts. Add ToDos

JulianFlesch
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Add nextflow_inspect to utils.

JulianFlesch
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Change return type of nextflow_inspect

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Don't ever return None from nextflow_inspect

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WIP module containers

JulianFlesch
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Lint mainnf container done

JulianFlesch
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Fix command creation and path for nextflow inspect

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

JulianFlesch
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output the summary of modules lint

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

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

JulianFlesch
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Remove conversion methods

JulianFlesch
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Adress container platform spelling ambiguities

JulianFlesch
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fix tests

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

ningyuxin1999
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mashehu
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add type hint and docstring
mashehu
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switch to "linux/a{rm,md}64" (slash-version) to avoid all the tooling
mashehu
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test with more realistic IDs (without platform info)
mashehu
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update uv.lock
mashehu
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switch container linting from fail to warn for now
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remove containers lint command, it is anyway part of `modules lint`
mashehu
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switch back to scan_id and build_id to keep in sync with schema
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replace progressbar with spinner
mashehu
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deprecate old container checks
mashehu
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move bioconda version checking to environment.yml checks
mashehu
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remove linting for conda-lock file urls
mashehu
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use key variables in test file to keep them in sync
mashehu
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simplify module parsing code
mashehu
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add local module container tests
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add per container spinner
mashehu
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fix meta yaml linting test
mashehu
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fix linting error
mashehu
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fix jinja variable in template
mashehu
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disable warning count until we migrate gitlab modules to containers
mashehu
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Conda lock files wip
JulianFlesch
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Commits on Apr 1, 2026

Merge branch 'dev' into feature/3952-create-waveyml
ningyuxin1999
authored

Commits on Apr 2, 2026

giga-merge. Adds linting docstring
JulianFlesch
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Commits

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