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[TheiaCoV/TheiaProk/TheiaMeta/TheiaEuk/Freyja_FASTQ] fastq-scan updates & improvements. Adding JSON as wf output file #1821

[TheiaCoV/TheiaProk/TheiaMeta/TheiaEuk/Freyja_FASTQ] fastq-scan updates & improvements. Adding JSON as wf output file

[TheiaCoV/TheiaProk/TheiaMeta/TheiaEuk/Freyja_FASTQ] fastq-scan updates & improvements. Adding JSON as wf output file #1821