New ivar_variants_to_vcf.py #176

Job	Run time
Test workflow parameters (--consensus_caller ivar)	12m 14s
Test Nanopore workflow (--gff false)	21m 38s
Test workflow parameters (--variant_caller bcftools --consensus_caller ivar)	2m 43s
Test Nanopore workflow (--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz)	22m 43s
Test Nanopore workflow (--input false)	22m 5s
Test Nanopore workflow (--min_barcode_reads 10000)	1m 38s
Test SISPA workflow (--gff false)	13m 37s
Test workflow parameters (--skip_fastp --skip_pangolin)	12m 13s
Run pipeline with test data (23.04.0)	21m 21s
Test SISPA workflow (--genome 'NC_045512.2')	14m 1s
Test Nanopore workflow (--min_guppyplex_reads 10000)	4m 0s
Run pipeline with test data (latest-everything)	21m 39s
Test Nanopore workflow (--artic_minion_caller medaka --sequencing_summary false --fast5_dir false)	27m 2s
Test workflow parameters (--skip_variants)	8m 59s
Test Nanopore workflow (--artic_minion_caller medaka --sequencing_summary false --fast5_dir false...	27m 16s
Test workflow parameters (--skip_cutadapt --skip_snpeff)	12m 6s
Test workflow parameters (--skip_kraken2)	12m 14s
Test workflow parameters (--skip_assembly)	11m 55s
Test workflow parameters (--spades_mode corona)	11m 48s
Test workflow parameters (--spades_mode metaviral)	10m 21s
Test workflow parameters (--skip_plasmidid false --skip_asciigenome)	10m 25s
Test workflow parameters (--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz)	12m 14s
	5h 14m 12s

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