New ivar_variants_to_vcf.py #182

Job	Run time
Run pipeline with test data (23.04.0)	17m 52s
Test workflow parameters (--consensus_caller ivar)	17m 52s
Run pipeline with test data (latest-everything)	17m 51s
Test Nanopore workflow (--gff false --freyja_depthcutoff 1)	16m 6s
Test workflow parameters (--variant_caller bcftools --consensus_caller ivar)	17m 51s
Test Nanopore workflow (--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz --fr...	17m 52s
Test Nanopore workflow (--input false --freyja_depthcutoff 1)	17m 50s
Test SISPA workflow (--gff false)	5m 53s
Test Nanopore workflow (--min_barcode_reads 10000)	1m 36s
Test SISPA workflow (--genome 'NC_045512.2')	14m 34s
Test Nanopore workflow (--min_guppyplex_reads 10000)	3m 42s
Test Nanopore workflow (--artic_minion_caller medaka --sequencing_summary false --fast5_dir false...	17m 51s
Test workflow parameters (--skip_fastp --skip_pangolin)	17m 52s
Test Nanopore workflow (--artic_minion_caller medaka --sequencing_summary false --fast5_dir false...	17m 51s
Test workflow parameters (--skip_variants)	11m 53s
Test workflow parameters (--skip_cutadapt --skip_snpeff)	17m 52s
Test workflow parameters (--skip_kraken2)	17m 52s
Test workflow parameters (--skip_assembly)	17m 49s
Test workflow parameters (--spades_mode corona)	17m 53s
Test workflow parameters (--spades_mode metaviral)	17m 51s
Test workflow parameters (--skip_plasmidid false --skip_asciigenome)	17m 53s
Test workflow parameters (--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz)	17m 53s
	5h 39m 29s

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