New ivar_variants_to_vcf.py #185

Job	Run time
Run pipeline with test data (23.04.0)	24m 25s
Run pipeline with test data (latest-everything)	25m 40s
Test workflow parameters (--consensus_caller ivar)	26m 15s
Test Nanopore workflow (--gff false --freyja_depthcutoff 1)	24m 40s
Test workflow parameters (--variant_caller bcftools --consensus_caller ivar)	20m 50s
Test SISPA workflow (--gff false)	13m 45s
Test Nanopore workflow (--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz --fr...	28m 25s
Test workflow parameters (--skip_fastp --skip_pangolin)	25m 13s
Test SISPA workflow (--genome 'NC_045512.2')	15m 1s
Test workflow parameters (--skip_variants)	8m 44s
Test Nanopore workflow (--input false --freyja_depthcutoff 1)	26m 7s
Test workflow parameters (--skip_cutadapt --skip_snpeff)	26m 28s
Test Nanopore workflow (--min_barcode_reads 10000)	1m 47s
Test workflow parameters (--skip_kraken2)	24m 25s
Test Nanopore workflow (--min_guppyplex_reads 10000)	3m 54s
Test workflow parameters (--skip_assembly)	20m 59s
Test Nanopore workflow (--artic_minion_caller medaka --sequencing_summary false --fast5_dir false...	31m 39s
Test workflow parameters (--spades_mode corona)	23m 52s
Test Nanopore workflow (--artic_minion_caller medaka --sequencing_summary false --fast5_dir false...	31m 38s
Test workflow parameters (--spades_mode metaviral)	25m 4s
Test workflow parameters (--skip_plasmidid false --skip_asciigenome)	26m 45s
Test workflow parameters (--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz)	24m 57s
	8h 0m 33s

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