Command to generate pipeline container config files#3955

Merged

mashehu merged 40 commits into

nf-core:devfrom

mirpedrol:pipeline-container-config-builder

Apr 24, 2026

Commits on Apr 24, 2026

initial functions to generate pipeline container config files

mirpedrol
authored and
mashehu
committed
generate all config files

mirpedrol
authored and
mashehu
committed
regenerate container config files when modules install, remove, update

mirpedrol
authored and
mashehu
committed
pass repo_path

mirpedrol
authored and
mashehu
committed
add tests

mirpedrol
authored and
mashehu
committed
less lines

mirpedrol
authored and
mashehu
committed
always update docker amd64

mirpedrol
authored and
mashehu
committed
Update nf_core/pipelines/containers_utils.py

mirpedrol
and
mashehu
committed
spaces

mirpedrol
authored and
mashehu
committed
Apply suggestions from code review

mirpedrol
and
mashehu
committed
fix types
mashehu
committed
inspect in json format and fix tests

mirpedrol
authored and
mashehu
committed
simplify functions, thanks @mashehu

mirpedrol
authored and
mashehu
committed
Update tests/pipelines/test_container_configs.py

mirpedrol
authored and
mashehu
committed
remove too many warnings and add debug messages and one info summary instead

mirpedrol
authored and
mashehu
committed
update arch names to make it consistent with modules container command
mashehu
committed
parse the include statements to get modules paths from process names
mashehu
committed
sort generated config files
mashehu
committed
drop `linux_` prefix of arch in config file names
mashehu
committed
Apply suggestions from code review
mashehu
committed
add container configs to linting
mashehu
committed
remove unused argument
mashehu
committed
remove org from containerconfigs
mashehu
committed
update template modules to latest version
mashehu
committed
fix container config test
mashehu
committed
bump nextflow version to 25.10.4
mashehu
committed
fix type warning
mashehu
committed
fix ruff linting errors
mashehu
committed
update modules.json in tempalte
mashehu
committed
fix todo hint
mashehu
committed
add container config creation step to template rendering
mashehu
committed
fix path to mock
mashehu
committed
fix tests by actually removing file that is now generated with pipelines create
mashehu
committed
more test fixes
mashehu
committed
move try_generate_container_configs to container_utils
mashehu
committed
use same PLATFORMS constant in containers_utils and tests
mashehu
committed
also regenerate container configs for patch commands
mashehu
committed
clean up container configs before writing new ones, to keep state in sync
mashehu
committed
manually add newly installed module to container config generator
mashehu
committed
update fastqc and multiqc to latest version
mashehu
committed