Fixing merge conflicts on #435 #193

Job	Run time
Run pipeline with test data (23.04.0)	7m 6s
Run pipeline with test data (latest-everything)	7m 25s
Test workflow parameters (--consensus_caller ivar)	6m 13s
Test SISPA workflow (--gff false)	13m 32s
Test workflow parameters (--variant_caller bcftools --consensus_caller ivar)	6m 13s
Test SISPA workflow (--genome 'NC_045512.2')	14m 24s
Test workflow parameters (--skip_fastp --skip_pangolin)	6m 18s
Test workflow parameters (--skip_variants)	6m 12s
Test workflow parameters (--skip_cutadapt --skip_snpeff)	6m 12s
Test workflow parameters (--skip_kraken2)	5m 55s
Test workflow parameters (--skip_assembly)	6m 14s
Test Nanopore workflow (--gff false --freyja_depthcutoff 1)	24m 16s
Test workflow parameters (--spades_mode corona)	6m 11s
Test Nanopore workflow (--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz --fr...	25m 42s
Test workflow parameters (--spades_mode metaviral)	6m 14s
Test Nanopore workflow (--input false --freyja_depthcutoff 1)	24m 54s
Test workflow parameters (--skip_plasmidid false --skip_asciigenome)	6m 13s
Test Nanopore workflow (--min_barcode_reads 10000)	1m 37s
Test workflow parameters (--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz)	6m 14s
Test Nanopore workflow (--min_guppyplex_reads 10000)	3m 21s
Test Nanopore workflow (--artic_minion_caller medaka --sequencing_summary false --fast5_dir false...	30m 40s
Test Nanopore workflow (--artic_minion_caller medaka --sequencing_summary false --fast5_dir false...	31m 22s
	4h 12m 28s

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