Resfinder improvements, added support for Shigella spp., added XDR Shigella prediction #482

Job	Run time
Check for changes	6s
tasks/assembly/task_dragonflye.wdl	23s
tasks/gene_typing/task_resfinder.wdl	23s
tasks/gene_typing/task_tiptoft.wdl	25s
tasks/phylogenetic_inference/task_lyveset.wdl	32s
tasks/quality_control/task_nanoplot.wdl	33s
tasks/quality_control/task_nanoq.wdl	21s
tasks/quality_control/task_screen.wdl	26s
tasks/species_typing/task_pangolin.wdl	22s
tasks/task_versioning.wdl	26s
tasks/taxon_id/task_gambit.wdl	20s
tasks/utilities/submission/task_gisaid_cli.wdl	31s
tasks/utilities/task_broad_terra_tools.wdl	22s
tasks/utilities/task_file_handling.wdl	22s
tasks/utilities/task_sra_fetch.wdl	26s
workflows/phylogenetics/wf_lyveset.wdl	32s
workflows/submission/wf_terra_2_gisaid.wdl	21s
workflows/theiacov/wf_theiacov_clearlabs.wdl	29s
workflows/theiacov/wf_theiacov_fasta.wdl	26s
workflows/theiacov/wf_theiacov_illumina_pe.wdl	22s
workflows/theiacov/wf_theiacov_illumina_se.wdl	39s
workflows/theiacov/wf_theiacov_ont.wdl	26s
workflows/theiaprok/wf_theiaprok_illumina_se.wdl	41s
workflows/theiaprok/wf_theiaprok_ont.wdl	25s
workflows/utilities/data_import/wf_sra_fetch.wdl	24s
workflows/utilities/wf_read_QC_trim_ont.wdl	26s
	11m 9s

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