New ivar_variants_to_vcf.py #186

Job	Run time
Test SISPA workflow (--gff false)	13m 32s
Test workflow parameters (--consensus_caller ivar)	24m 50s
Run pipeline with test data (23.04.0)	28m 27s
Test SISPA workflow (--genome 'NC_045512.2')	14m 25s
Test Nanopore workflow (--gff false --freyja_depthcutoff 1)	26m 6s
Test workflow parameters (--variant_caller bcftools --consensus_caller ivar)	24m 25s
Run pipeline with test data (latest-everything)	25m 32s
Test workflow parameters (--skip_fastp --skip_pangolin)	25m 20s
Test Nanopore workflow (--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz --fr...	26m 37s
Test workflow parameters (--skip_variants)	10m 25s
Test Nanopore workflow (--input false --freyja_depthcutoff 1)	25m 30s
Test Nanopore workflow (--min_barcode_reads 10000)	1m 39s
Test workflow parameters (--skip_cutadapt --skip_snpeff)	23m 38s
Test Nanopore workflow (--min_guppyplex_reads 10000)	3m 48s
Test workflow parameters (--skip_kraken2)	26m 12s
Test workflow parameters (--skip_assembly)	19m 15s
Test Nanopore workflow (--artic_minion_caller medaka --sequencing_summary false --fast5_dir false...	32m 13s
Test workflow parameters (--spades_mode corona)	24m 16s
Test Nanopore workflow (--artic_minion_caller medaka --sequencing_summary false --fast5_dir false...	31m 35s
Test workflow parameters (--spades_mode metaviral)	27m 2s
Test workflow parameters (--skip_plasmidid false --skip_asciigenome)	27m 44s
Test workflow parameters (--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz)	25m 22s
	8h 7m 53s

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