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DATAOPS-716 Use customized list of adapters, FastQC #60

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merged 4 commits into from
Jun 28, 2024

Commits on Jun 26, 2024

  1. Use customized list of adapters, FastQC

    When hoovering over the adapter content plot in the the FastQC output
    displayed in the end of all seqreports the name of the adapter found
    is appearing. The adapters and names used are by default the ones
    specified in the FastQC software. However, the provided list is outdated
    and many of the adapters are used in several library preparation kits. A
    customized list can now be used as input instead to look for adapters we
    use at SNP&SEQ and to display relevant names when found.
    
    Files changed:
    - New file, adapter_list_fastqc.txt, added in config/tool_config/ to
      specify the adapters to look for.
    - The fastqc command in main.nf is now updated with the additional
      a-flag that is used to specify the use of the file described under the
    previous point.
    monikaBrandt committed Jun 26, 2024
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Commits on Jun 27, 2024

  1. Update config/tool_config/adapter_list_fastqc.txt

    Co-authored-by: Matilda Åslin <[email protected]>
    monikaBrandt and matrulda authored Jun 27, 2024
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  2. Update config/tool_config/adapter_list_fastqc.txt

    Co-authored-by: Matilda Åslin <[email protected]>
    monikaBrandt and matrulda authored Jun 27, 2024
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  3. Configuration menu
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