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ngs_data_qc - pydantic throws error when parameters for picard are not defined #556

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mbenary opened this issue Dec 2, 2024 · 0 comments

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@mbenary
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mbenary commented Dec 2, 2024

Describe the bug
When running ngs_data_qc only with fastqc then pydantic throws an error which is related to Picard settings.

To Reproduce
Steps to reproduce the behavior:

step_config:
  ngs_data_qc:
    tools: [fastqc]
    fastqc: {}

snappy-snake -nrp
image

Expected behavior
No error should be thrown and fastqc should be able to run.

Additional context
In init.py Picard needs to be defined independent of the configuration file. A quick workaround is a change in the config:

  ngs_data_qc:
    tools: [fastqc]
    picard:
      programs:
        - CollectAlignmentSummaryMetrics
    fastqc: {}
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