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build seqera containers on modules create and modules bump-version #4362

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build seqera containers on modules create and modules bump-version #4362

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3909bcb
buildcontainers on module create
mashehu Jun 29, 2026
6139791
also use wave for bump-version
mashehu Jun 30, 2026
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67 changes: 8 additions & 59 deletions nf_core/commands_modules.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,6 @@

import rich

from nf_core.pipelines.containers_utils import try_generate_container_configs
from nf_core.utils import CONTAINER_PLATFORMS, rich_force_colors

log = logging.getLogger(__name__)
Expand Down Expand Up @@ -341,12 +340,7 @@ def modules_containers_create(ctx, module: str, directory: Path, force: bool) ->
"""
Build docker and singularity containers for linux/arm64 and linux/amd64 using wave.
"""
from rich.console import Group
from rich.live import Live
from rich.progress import BarColumn, MofNCompleteColumn, Progress, SpinnerColumn, TextColumn

from nf_core.modules.containers import ModuleContainers
from nf_core.pipelines.lint_utils import console
from nf_core.modules.containers import ModuleContainers, build_containers_with_progress

try:
manager = ModuleContainers(module=module, directory=directory, verbose=ctx.obj["verbose"])
Expand All @@ -364,60 +358,15 @@ def modules_containers_create(ctx, module: str, directory: Path, force: bool) ->
assert manager.nfcore_component is not None
components = [manager.nfcore_component]

failed_modules = []

overall_progress = Progress(
"[bold blue]{task.description}",
BarColumn(),
MofNCompleteColumn(),
console=console,
disable=ctx.obj["hide_progress"],
)
module_progress = Progress(
SpinnerColumn(finished_text="[green]✓[/green]"),
"[bold blue]{task.description}",
TextColumn("{task.fields[status]}"),
console=console,
disable=ctx.obj["hide_progress"],
failed_modules = build_containers_with_progress(
manager,
components,
directory,
force=force,
hide_progress=ctx.obj["hide_progress"],
verbose=ctx.obj["verbose"],
)

with Live(Group(overall_progress, module_progress), console=console, transient=True):
# The overall bar is only useful when processing more than one module
overall_task_id = overall_progress.add_task("modules", total=len(components), visible=len(components) > 1)
for component in components:
module_name = component.component_name
module_task_id = module_progress.add_task(
f"[cyan]{module_name}[/cyan]",
total=None,
status="building containers...",
)
try:
if manager.all_modules:
# Per-module instance, reusing the already-scanned component list
module_manager = ModuleContainers(
module=module_name,
directory=directory,
verbose=ctx.obj["verbose"],
components=manager.available_modules,
)
else:
module_manager = manager
_, success = module_manager.create(
progress_bar=module_progress, task_id=module_task_id, force=force
)
if success:
module_manager.update_containers_in_meta()
if module_manager.repo_type == "pipeline":
try_generate_container_configs(directory, module_manager.module_directory)
else:
failed_modules.append(module_name)
except (ValueError, RuntimeError, OSError) as e:
log.error(f"✗ Failed to build containers for {module_name}: {e}")
failed_modules.append(module_name)
finally:
overall_progress.advance(overall_task_id)
module_progress.remove_task(module_task_id)

if failed_modules:
if manager.all_modules:
log.warning(
Expand Down
45 changes: 29 additions & 16 deletions nf_core/components/create.py
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Original file line number Diff line number Diff line change
Expand Up @@ -177,8 +177,37 @@ def create(self) -> bool:
run_prettier_on_file(new_files)

log.info("Created following files:\n " + "\n ".join(new_files))

if self.component_type == "modules":
self._build_seqera_containers()

return True

def _build_seqera_containers(self) -> None:
"""
Build Seqera/Wave containers for the freshly created module.
"""
from nf_core.modules.containers import ModuleContainers, build_containers_with_progress

log.info("Building Seqera containers for the module with Wave...")
try:
manager = ModuleContainers(
module=self.component_name,
directory=self.directory,
)
ModuleContainers.check_tower_token()
if manager.nfcore_component is None:
log.warning("Could not locate the new module to build Seqera containers.")
return
failed = build_containers_with_progress(manager, [manager.nfcore_component], self.directory)
if failed:
log.warning(
"Could not build all Seqera containers for the module. "
"Run `nf-core modules containers create` to retry."
)
except (ValueError, RuntimeError, OSError) as e:
log.warning(f"Could not build Seqera containers for the module: {e}")

def _get_bioconda_tool(self):
"""
Try to find a bioconda package for 'tool'
Expand Down Expand Up @@ -226,22 +255,6 @@ def _get_bioconda_tool(self):
)
break

# Try to get the container tag (only if bioconda package was found)
if self.bioconda:
try:
if self.tool_conda_name:
self.docker_container, self.singularity_container = nf_core.utils.get_biocontainer_tag(
self.tool_conda_name, version
)
else:
self.docker_container, self.singularity_container = nf_core.utils.get_biocontainer_tag(
self.component, version
)
log.info(f"Using Docker container: '{self.docker_container}'")
log.info(f"Using Singularity container: '{self.singularity_container}'")
except (ValueError, LookupError) as e:
log.info(f"Could not find a Docker/Singularity container ({e})")

def _get_module_structure_components(self):
process_label_defaults = [
"process_single",
Expand Down
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