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Merge pull request #455 from heuermh/merging-template-updates #1367

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Merge pull request #455 from heuermh/merging-template-updates

Merge pull request #455 from heuermh/merging-template-updates #1367

Run time

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Job Run time
Run pipeline with test data (24.04.2 | test | docker)
30m 49s
Test nanopore (24.04.2 | --gff false --freyja_depthcutoff 1 | docker)
22m 45s
Run pipeline with test data (latest-everything | test | docker)
31m 8s
Test nanopore (24.04.2 | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz --freyja_depthcutoff 1 | docker)
26m 42s
Test parameters (24.04.2 | --consensus_caller ivar | docker)
32m 37s
Test nanopore (24.04.2 | --input false --freyja_depthcutoff 1 | docker)
25m 43s
Test parameters (24.04.2 | --variant_caller bcftools --consensus_caller ivar | docker)
29m 35s
Test SISPA (24.04.2 | --gff false | docker)
22m 25s
Test nanopore (24.04.2 | --min_barcode_reads 10000 | docker)
5m 30s
Test parameters (24.04.2 | --skip_fastp --skip_pangolin | docker)
32m 5s
Test nanopore (24.04.2 | --min_guppyplex_reads 10000 | docker)
7m 50s
Test parameters (24.04.2 | --skip_variants | docker)
11m 27s
Test nanopore (24.04.2 | --artic_minion_caller medaka --sequencing_summary false --fast5_dir false --freyja_depthcutoff 1 | docker)
40m 26s
Test SISPA (24.04.2 | --genome 'NC_045512.2' | docker)
26m 22s
Test parameters (24.04.2 | --skip_cutadapt --skip_snpeff | docker)
30m 57s
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)
38m 4s
Test SISPA (latest-everything | --gff false | docker)
22m 8s
Test parameters (24.04.2 | --skip_kraken2 | docker)
33m 45s
Test nanopore (latest-everything | --gff false --freyja_depthcutoff 1 | docker)
23m 33s
Test SISPA (latest-everything | --genome 'NC_045512.2' | docker)
25m 5s
Test parameters (24.04.2 | --skip_assembly | docker)
25m 41s
Test nanopore (latest-everything | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz --freyja_depthcutoff 1 | docker)
25m 13s
Test parameters (24.04.2 | --spades_mode corona | docker)
33m 26s
Test nanopore (latest-everything | --input false --freyja_depthcutoff 1 | docker)
24m 14s
Test parameters (24.04.2 | --spades_mode metaviral | docker)
31m 48s
Test nanopore (latest-everything | --min_barcode_reads 10000 | docker)
4m 54s
Test parameters (24.04.2 | --skip_plasmidid false --skip_asciigenome | docker)
35m 50s
Test nanopore (latest-everything | --min_guppyplex_reads 10000 | docker)
8m 39s
Test parameters (24.04.2 | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz | docker)
32m 21s
Test nanopore (latest-everything | --artic_minion_caller medaka --sequencing_summary false --fast5_dir false --freyja_depthcutoff 1 | docker)
38m 22s
Test parameters (24.04.2 | --bowtie2_index ./GCA_009858895.3_ASM985889v3_genomic.200409.bt2.index.tar.gz | docker)
31m 45s
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)
40m 3s
Test parameters (24.04.2 | --skip_noninternal_primers --threeprime_adapters | docker)
30m 29s
Test parameters (latest-everything | --consensus_caller ivar | docker)
31m 58s
Test parameters (latest-everything | --variant_caller bcftools --consensus_caller ivar | docker)
31m 26s
Test parameters (latest-everything | --skip_fastp --skip_pangolin | docker)
31m 3s
Test parameters (latest-everything | --skip_variants | docker)
13m 11s
Test parameters (latest-everything | --skip_cutadapt --skip_snpeff | docker)
32m 32s
Test parameters (latest-everything | --skip_kraken2 | docker)
31m 53s
Test parameters (latest-everything | --skip_assembly | docker)
26m 31s
Test parameters (latest-everything | --spades_mode corona | docker)
31m 10s
Test parameters (latest-everything | --spades_mode metaviral | docker)
30m 21s
Test parameters (latest-everything | --skip_plasmidid false --skip_asciigenome | docker)
36m 35s
Test parameters (latest-everything | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz | docker)
31m 9s
Test parameters (latest-everything | --bowtie2_index ./GCA_009858895.3_ASM985889v3_genomic.200409.bt2.index.tar.gz | docker)
32m 23s
Test parameters (latest-everything | --skip_noninternal_primers --threeprime_adapters | docker)
28m 27s
21h 10m 20s