New ivar_variants_to_vcf.py #184

Job	Run time
Run pipeline with test data (23.04.0)	26m 17s
Test Nanopore workflow (--gff false --freyja_depthcutoff 1)	25m 38s
Run pipeline with test data (latest-everything)	25m 3s
Test workflow parameters (--consensus_caller ivar)	31m 34s
Test Nanopore workflow (--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz --fr...	26m 32s
Test workflow parameters (--variant_caller bcftools --consensus_caller ivar)	24m 29s
Test Nanopore workflow (--input false --freyja_depthcutoff 1)	26m 40s
Test workflow parameters (--skip_fastp --skip_pangolin)	25m 52s
Test Nanopore workflow (--min_barcode_reads 10000)	1m 39s
Test SISPA workflow (--gff false)	14m 16s
Test workflow parameters (--skip_variants)	10m 39s
Test SISPA workflow (--genome 'NC_045512.2')	14m 52s
Test Nanopore workflow (--min_guppyplex_reads 10000)	6m 10s
Test Nanopore workflow (--artic_minion_caller medaka --sequencing_summary false --fast5_dir false...	31m 52s
Test workflow parameters (--skip_cutadapt --skip_snpeff)	23m 28s
Test Nanopore workflow (--artic_minion_caller medaka --sequencing_summary false --fast5_dir false...	30m 49s
Test workflow parameters (--skip_kraken2)	25m 8s
Test workflow parameters (--skip_assembly)	19m 53s
Test workflow parameters (--spades_mode corona)	25m 38s
Test workflow parameters (--spades_mode metaviral)	24m 44s
Test workflow parameters (--skip_plasmidid false --skip_asciigenome)	26m 38s
Test workflow parameters (--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz)	25m 45s
	8h 13m 36s

Provide feedback