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fix cardinality when params.bowtie2_index used #1339

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fix cardinality when params.bowtie2_index used

fix cardinality when params.bowtie2_index used #1339

Run time

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Job Run time
Run pipeline with test data (23.04.0)
29m 4s
Test workflow parameters (--consensus_caller ivar)
4m 4s
Run pipeline with test data (latest-everything)
25m 18s
Test Nanopore workflow (--gff false --freyja_depthcutoff 1)
23m 31s
Test workflow parameters (--variant_caller bcftools --consensus_caller ivar)
4m 3s
Test Nanopore workflow (--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz --fr...
26m 12s
Test workflow parameters (--skip_fastp --skip_pangolin)
4m 5s
Test Nanopore workflow (--input false --freyja_depthcutoff 1)
25m 0s
Test SISPA workflow (--gff false)
13m 47s
Test workflow parameters (--skip_variants)
3m 56s
Test Nanopore workflow (--min_barcode_reads 10000)
1m 36s
Test SISPA workflow (--genome 'NC_045512.2')
14m 40s
Test workflow parameters (--skip_cutadapt --skip_snpeff)
4m 5s
Test Nanopore workflow (--min_guppyplex_reads 10000)
3m 44s
Test workflow parameters (--skip_kraken2)
4m 4s
Test Nanopore workflow (--artic_minion_caller medaka --sequencing_summary false --fast5_dir false...
31m 38s
Test workflow parameters (--skip_assembly)
3m 53s
Test Nanopore workflow (--artic_minion_caller medaka --sequencing_summary false --fast5_dir false...
33m 9s
Test workflow parameters (--spades_mode corona)
4m 8s
Test workflow parameters (--spades_mode metaviral)
4m 4s
Test workflow parameters (--skip_plasmidid false --skip_asciigenome)
4m 6s
Test workflow parameters (--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz)
4m 5s
Test workflow parameters (--bowtie2_index ./GCA_009858895.3_ASM985889v3_genomic.200409.bt2.index....
3m 46s
4h 35m 58s