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Patch nf schema - include integer & string as type for sample #1354

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Patch nf schema - include integer & string as type for sample

Patch nf schema - include integer & string as type for sample #1354

Run time

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Job Run time
Run pipeline with test data (24.04.2 | test | docker)
3m 33s
Test nanopore (24.04.2 | --gff false --freyja_depthcutoff 1 | docker)
3m 31s
Run pipeline with test data (latest-everything | test | docker)
3m 32s
Test nanopore (24.04.2 | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz --freyja_depthcutoff 1 | docker)
3m 30s
Test parameters (24.04.2 | --consensus_caller ivar | docker)
3m 21s
Test nanopore (24.04.2 | --input false --freyja_depthcutoff 1 | docker)
3m 31s
Test parameters (24.04.2 | --variant_caller bcftools --consensus_caller ivar | docker)
2m 45s
Test SISPA (24.04.2 | --gff false | docker)
3m 33s
Test parameters (24.04.2 | --skip_fastp --skip_pangolin | docker)
3m 7s
Test nanopore (24.04.2 | --min_barcode_reads 10000 | docker)
3m 31s
Test SISPA (24.04.2 | --genome 'NC_045512.2' | docker)
3m 30s
Test nanopore (24.04.2 | --min_guppyplex_reads 10000 | docker)
3m 30s
Test parameters (24.04.2 | --skip_variants | docker)
2m 59s
Test SISPA (latest-everything | --gff false | docker)
3m 30s
Test nanopore (24.04.2 | --artic_minion_caller medaka --sequencing_summary false --fast5_dir false --freyja_depthcutoff 1 | docker)
3m 30s
Test parameters (24.04.2 | --skip_cutadapt --skip_snpeff | docker)
3m 9s
Test SISPA (latest-everything | --genome 'NC_045512.2' | docker)
3m 30s
Test parameters (24.04.2 | --skip_kraken2 | docker)
3m 3s
Test nanopore (24.04.2 | --artic_minion_caller medaka --sequencing_summary false --fast5_dir false --artic_minion_medaka_model ./r941_min_high_g360_model.hdf5 --freyja_depthcutoff 1 | docker)
3m 33s
Test parameters (24.04.2 | --skip_assembly | docker)
3m 9s
Test nanopore (latest-everything | --gff false --freyja_depthcutoff 1 | docker)
2m 42s
Test parameters (24.04.2 | --spades_mode corona | docker)
2m 52s
Test nanopore (latest-everything | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz --freyja_depthcutoff 1 | docker)
3m 29s
Test nanopore (latest-everything | --input false --freyja_depthcutoff 1 | docker)
3m 29s
Test parameters (24.04.2 | --spades_mode metaviral | docker)
2m 58s
Test nanopore (latest-everything | --min_barcode_reads 10000 | docker)
3m 30s
Test parameters (24.04.2 | --skip_plasmidid false --skip_asciigenome | docker)
2m 58s
Test nanopore (latest-everything | --min_guppyplex_reads 10000 | docker)
3m 34s
Test parameters (24.04.2 | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz | docker)
3m 29s
Test parameters (24.04.2 | --bowtie2_index ./GCA_009858895.3_ASM985889v3_genomic.200409.bt2.index.tar.gz | docker)
3m 21s
Test nanopore (latest-everything | --artic_minion_caller medaka --sequencing_summary false --fast5_dir false --freyja_depthcutoff 1 | docker)
3m 30s
Test parameters (24.04.2 | --skip_noninternal_primers --threeprime_adapters | docker)
3m 1s
Test nanopore (latest-everything | --artic_minion_caller medaka --sequencing_summary false --fast5_dir false --artic_minion_medaka_model ./r941_min_high_g360_model.hdf5 --freyja_depthcutoff 1 | docker)
3m 31s
Test parameters (latest-everything | --consensus_caller ivar | docker)
1m 47s
Test parameters (latest-everything | --variant_caller bcftools --consensus_caller ivar | docker)
2m 19s
Test parameters (latest-everything | --skip_fastp --skip_pangolin | docker)
2m 15s
Test parameters (latest-everything | --skip_variants | docker)
2m 14s
Test parameters (latest-everything | --skip_cutadapt --skip_snpeff | docker)
2m 8s
Test parameters (latest-everything | --skip_kraken2 | docker)
2m 14s
Test parameters (latest-everything | --skip_assembly | docker)
2m 18s
Test parameters (latest-everything | --spades_mode corona | docker)
2m 1s
Test parameters (latest-everything | --spades_mode metaviral | docker)
1m 45s
Test parameters (latest-everything | --skip_plasmidid false --skip_asciigenome | docker)
2m 36s
Test parameters (latest-everything | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz | docker)
2m 36s
Test parameters (latest-everything | --bowtie2_index ./GCA_009858895.3_ASM985889v3_genomic.200409.bt2.index.tar.gz | docker)
2m 18s
Test parameters (latest-everything | --skip_noninternal_primers --threeprime_adapters | docker)
2m 25s
2h 18m 37s