New ivar_variants_to_vcf.py #187

Job	Run time
Run pipeline with test data (23.04.0)	23m 39s
Test Nanopore workflow (--gff false --freyja_depthcutoff 1)	23m 44s
Run pipeline with test data (latest-everything)	26m 26s
Test Nanopore workflow (--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz --fr...	28m 34s
Test workflow parameters (--consensus_caller ivar)	24m 6s
Test workflow parameters (--variant_caller bcftools --consensus_caller ivar)	23m 37s
Test Nanopore workflow (--input false --freyja_depthcutoff 1)	26m 6s
Test workflow parameters (--skip_fastp --skip_pangolin)	24m 47s
Test SISPA workflow (--gff false)	14m 2s
Test workflow parameters (--skip_variants)	10m 40s
Test Nanopore workflow (--min_barcode_reads 10000)	1m 44s
Test SISPA workflow (--genome 'NC_045512.2')	14m 21s
Test workflow parameters (--skip_cutadapt --skip_snpeff)	23m 18s
Test Nanopore workflow (--min_guppyplex_reads 10000)	4m 50s
Test workflow parameters (--skip_kraken2)	25m 28s
Test workflow parameters (--skip_assembly)	21m 13s
Test Nanopore workflow (--artic_minion_caller medaka --sequencing_summary false --fast5_dir false...	34m 2s
Test workflow parameters (--spades_mode corona)	26m 5s
Test Nanopore workflow (--artic_minion_caller medaka --sequencing_summary false --fast5_dir false...	31m 36s
Test workflow parameters (--spades_mode metaviral)	24m 27s
Test workflow parameters (--skip_plasmidid false --skip_asciigenome)	25m 17s
Test workflow parameters (--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz)	26m 28s
	8h 4m 30s

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