[TheiaCoV/TheiaProk/TheiaMeta/TheiaEuk/Freyja_FASTQ] `fastq-scan` updates & improvements. Adding JSON as wf output file #1891

Job	Run time
Check for changes	5s
tasks/quality_control/basic_statistics/task_fastq_scan.wdl	18s
tasks/utilities/data_export/task_broad_terra_tools.wdl	18s
workflows/freyja/wf_freyja_fastq.wdl	22s
workflows/theiacov/wf_theiacov_clearlabs.wdl	18s
workflows/theiacov/wf_theiacov_illumina_pe.wdl	18s
workflows/theiacov/wf_theiacov_illumina_se.wdl	26s
workflows/theiaeuk/wf_theiaeuk_illumina_pe.wdl	20s
workflows/theiameta/wf_theiameta_illumina_pe.wdl	17s
workflows/theiaprok/wf_theiaprok_illumina_pe.wdl	30s
workflows/theiaprok/wf_theiaprok_illumina_se.wdl	30s
workflows/utilities/wf_read_QC_trim_ont.wdl	19s
workflows/utilities/wf_read_QC_trim_pe.wdl	16s
workflows/utilities/wf_read_QC_trim_se.wdl	17s
	4m 34s

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