New ivar_variants_to_vcf.py #183

Job	Run time
Test Nanopore workflow (--gff false --freyja_depthcutoff 1)	23m 59s
Test workflow parameters (--consensus_caller ivar)	26m 8s
Test Nanopore workflow (--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz --fr...	25m 48s
Run pipeline with test data (23.04.0)	26m 54s
Test SISPA workflow (--gff false)	13m 56s
Test Nanopore workflow (--input false --freyja_depthcutoff 1)	24m 35s
Test workflow parameters (--variant_caller bcftools --consensus_caller ivar)	24m 35s
Run pipeline with test data (latest-everything)	25m 39s
Test SISPA workflow (--genome 'NC_045512.2')	16m 1s
Test Nanopore workflow (--min_barcode_reads 10000)	1m 39s
Test workflow parameters (--skip_fastp --skip_pangolin)	26m 22s
Test Nanopore workflow (--min_guppyplex_reads 10000)	3m 38s
Test workflow parameters (--skip_variants)	16m 38s
Test Nanopore workflow (--artic_minion_caller medaka --sequencing_summary false --fast5_dir false...	32m 23s
Test workflow parameters (--skip_cutadapt --skip_snpeff)	24m 30s
Test Nanopore workflow (--artic_minion_caller medaka --sequencing_summary false --fast5_dir false...	31m 31s
Test workflow parameters (--skip_kraken2)	25m 56s
Test workflow parameters (--skip_assembly)	30m 32s
Test workflow parameters (--spades_mode corona)	25m 17s
Test workflow parameters (--spades_mode metaviral)	26m 9s
Test workflow parameters (--skip_plasmidid false --skip_asciigenome)	31m 33s
Test workflow parameters (--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz)	25m 37s
	8h 29m 20s

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