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Merge pull request #439 from nf-core/bowtie-index-cardinality #1341

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Merge pull request #439 from nf-core/bowtie-index-cardinality

Merge pull request #439 from nf-core/bowtie-index-cardinality #1341

Run time

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Job Run time
Run pipeline with test data (23.04.0)
23m 47s
Test workflow parameters (--consensus_caller ivar)
23m 42s
Test Nanopore workflow (--gff false --freyja_depthcutoff 1)
23m 52s
Run pipeline with test data (latest-everything)
24m 4s
Test workflow parameters (--variant_caller bcftools --consensus_caller ivar)
23m 32s
Test Nanopore workflow (--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz --fr...
25m 30s
Test workflow parameters (--skip_fastp --skip_pangolin)
24m 43s
Test Nanopore workflow (--input false --freyja_depthcutoff 1)
25m 19s
Test SISPA workflow (--gff false)
13m 32s
Test workflow parameters (--skip_variants)
9m 6s
Test Nanopore workflow (--min_barcode_reads 10000)
1m 32s
Test SISPA workflow (--genome 'NC_045512.2')
13m 47s
Test workflow parameters (--skip_cutadapt --skip_snpeff)
24m 36s
Test Nanopore workflow (--min_guppyplex_reads 10000)
3m 23s
Test workflow parameters (--skip_kraken2)
24m 53s
Test Nanopore workflow (--artic_minion_caller medaka --sequencing_summary false --fast5_dir false...
31m 28s
Test workflow parameters (--skip_assembly)
19m 29s
Test Nanopore workflow (--artic_minion_caller medaka --sequencing_summary false --fast5_dir false...
31m 17s
Test workflow parameters (--spades_mode corona)
24m 18s
Test workflow parameters (--spades_mode metaviral)
25m 23s
Test workflow parameters (--skip_plasmidid false --skip_asciigenome)
25m 32s
Test workflow parameters (--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz)
24m 15s
Test workflow parameters (--bowtie2_index ./GCA_009858895.3_ASM985889v3_genomic.200409.bt2.index....
25m 11s
8h 12m 11s