Fix: nextflow inspect not resolving config-based container overrides
#6736
+45
−16
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…extflow-io#6734) The `nextflow inspect` command was returning containers defined in process source files instead of the overridden values from profile configuration files (e.g., withName selectors). Root cause: In ProcessDef.createTaskProcessor(), the condition `if( !processConfig )` was meant to call initialize() if config wasn't set, but processConfig is always non-empty (initialized with DEFAULT_CONFIG values in the constructor), so initialize() was never called through this code path. The initialize() method is responsible for applying config file settings (withName/withLabel selectors) to the process config, including container overrides. Fix: - Add an `initialized` flag to track whether config has been applied - Make initialize() idempotent by checking the flag - Always call initialize() in createTaskProcessor() (safe due to idempotency) - Reset initialized flag in clone() so cloned processes can be re-initialized This ensures that when ContainersInspector calls createTaskProcessor() to create task previews, the config file settings are properly applied first. Signed-off-by: Claude <noreply@anthropic.com>
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bentsherman
approved these changes
Jan 20, 2026
jorgee
approved these changes
Jan 20, 2026
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Fixes #6734
The
nextflow inspectcommand was returning containers defined in process source files instead of the overridden values from profile configuration files (e.g., withName selectors).Root cause: In ProcessDef.createTaskProcessor(), the condition
if( !processConfig )was meant to callinitialize()if config wasn't set:nextflow/modules/nextflow/src/main/groovy/nextflow/script/ProcessDef.groovy
Lines 263 to 265 in 24cc59e
But
processConfigis always non-empty (initialized withDEFAULT_CONFIGvalues in the constructor), soinitialize()was never called through this code path.The
initialize() method is responsible for applying config file settings (withName/withLabel` selectors) to the process config, including container overrides.Fix:
initializedflag to track whether config has been appliedinitialize()idempotent by checking the flaginitialize()increateTaskProcessor()(safe due to idempotency)clone()so cloned processes can be re-initializedThis ensures that when
ContainersInspectorcallscreateTaskProcessor()to create task previews, the config file settings are properly applied first.