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Added option to add a custom annotation, clarified multiQC results and fixed issues #1305

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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 #1305

Run time

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Job Run time
Test Nanopore workflow (--gff false)
21m 2s
Test Nanopore workflow (--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz)
21m 46s
Test Nanopore workflow (--input false)
20m 32s
Test Nanopore workflow (--min_barcode_reads 10000)
1m 37s
Test SISPA workflow (--gff false)
13m 38s
Test Nanopore workflow (--min_guppyplex_reads 10000)
3m 34s
Run pipeline with test data (23.04.0)
22m 52s
Test SISPA workflow (--genome 'NC_045512.2')
13m 50s
Test Nanopore workflow (--artic_minion_caller medaka --sequencing_summary false --fast5_dir false)
27m 10s
Run pipeline with test data (latest-everything)
23m 19s
Test workflow parameters (--consensus_caller ivar)
23m 8s
Test workflow parameters (--variant_caller bcftools --consensus_caller ivar)
22m 37s
Test workflow parameters (--skip_fastp --skip_pangolin)
24m 2s
Test workflow parameters (--skip_variants)
9m 5s
Test Nanopore workflow (--artic_minion_caller medaka --sequencing_summary false --fast5_dir false...
27m 14s
Test workflow parameters (--skip_cutadapt --skip_snpeff)
22m 29s
Test workflow parameters (--skip_kraken2)
23m 47s
Test workflow parameters (--skip_assembly)
19m 24s
Test workflow parameters (--spades_mode corona)
25m 33s
Test workflow parameters (--spades_mode metaviral)
23m 8s
Test workflow parameters (--skip_plasmidid false --skip_asciigenome)
31m 56s
Test workflow parameters (--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz)
25m 34s
7h 27m 17s