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Added option to add a custom annotation, clarified multiQC results and fixed issues #1307

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Added option to add a custom annotation, clarified multiQC results and fixed issues

Added option to add a custom annotation, clarified multiQC results and fixed issues #1307

Run time

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Job Run time
Run pipeline with test data (23.04.0)
24m 41s
Test Nanopore workflow (--gff false)
20m 35s
Test workflow parameters (--consensus_caller ivar)
25m 11s
Test Nanopore workflow (--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz)
28m 4s
Test workflow parameters (--variant_caller bcftools --consensus_caller ivar)
22m 25s
Test Nanopore workflow (--input false)
21m 5s
Test workflow parameters (--skip_fastp --skip_pangolin)
24m 21s
Test Nanopore workflow (--min_barcode_reads 10000)
1m 53s
Test workflow parameters (--skip_variants)
9m 31s
Test Nanopore workflow (--min_guppyplex_reads 10000)
3m 50s
Run pipeline with test data (latest-everything)
24m 11s
Test workflow parameters (--skip_cutadapt --skip_snpeff)
22m 54s
Test Nanopore workflow (--artic_minion_caller medaka --sequencing_summary false --fast5_dir false)
26m 32s
Test workflow parameters (--skip_kraken2)
23m 52s
Test Nanopore workflow (--artic_minion_caller medaka --sequencing_summary false --fast5_dir false...
27m 7s
Test SISPA workflow (--gff false)
13m 25s
Test workflow parameters (--skip_assembly)
20m 11s
Test workflow parameters (--spades_mode corona)
23m 30s
Test SISPA workflow (--genome 'NC_045512.2')
13m 55s
Test workflow parameters (--spades_mode metaviral)
27m 2s
Test workflow parameters (--skip_plasmidid false --skip_asciigenome)
33m 13s
Test workflow parameters (--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz)
24m 59s
7h 42m 27s