Fix module run crash with multi-output processes#6965
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ProcessEntryHandler.printOutput() assumed all output channels were DataflowVariable, but processes with multiple outputs use DataflowBroadcast. Use CH.getReadChannel() to handle both channel types and subscribe read channels before the dataflow network fires. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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Adding tests data |
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Both PRs (this and #6875) works fine for nf-core/fastqc. For salmon/quant they have the same problem with alignemt mode boolean, that we need to cast to boolean |
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Closing in favor of #6875 |
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Summary
GroovyCastExceptionwhen runningnextflow module runon processes with multiple output channels (e.g.nf-core/fastqc)ProcessEntryHandler.printOutput()assumed all output channels wereDataflowVariable, but processes with multiple outputs useDataflowBroadcastCH.getReadChannel()to handle both channel types and subscribe read channels before the dataflow network firesFixes #6958
Supersedes #6963
Test plan
createReadChannelscorrectly handles mixedDataflowVariableandDataflowBroadcastchannelsnextflow module run nf-core/fastqcand verify no cast error