[TheiaCoV/TheiaProk/TheiaMeta/TheiaEuk/Freyja_FASTQ] `fastq-scan` updates & improvements. Adding JSON as wf output file #1853

Job	Run time
Check for changes	4s
tasks/quality_control/basic_statistics/task_fastq_scan.wdl	20s
tasks/utilities/data_export/task_broad_terra_tools.wdl	24s
workflows/freyja/wf_freyja_fastq.wdl	19s
workflows/theiacov/wf_theiacov_clearlabs.wdl	17s
workflows/theiacov/wf_theiacov_illumina_pe.wdl	24s
workflows/theiacov/wf_theiacov_illumina_se.wdl	23s
workflows/theiaeuk/wf_theiaeuk_illumina_pe.wdl	35s
workflows/theiameta/wf_theiameta_illumina_pe.wdl	22s
workflows/theiaprok/wf_theiaprok_illumina_pe.wdl	27s
workflows/theiaprok/wf_theiaprok_illumina_se.wdl	25s
workflows/utilities/wf_read_QC_trim_ont.wdl	23s
workflows/utilities/wf_read_QC_trim_pe.wdl	22s
workflows/utilities/wf_read_QC_trim_se.wdl	23s
	5m 8s

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