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Merging 3.1.0 and 3.1.1 template updates #1364

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Merging 3.1.0 and 3.1.1 template updates

Merging 3.1.0 and 3.1.1 template updates #1364

Run time

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Job Run time
Test SISPA (24.04.2 | --gff false | docker)
21m 4s
Test SISPA (24.04.2 | --genome 'NC_045512.2' | docker)
22m 25s
Test parameters (24.04.2 | --consensus_caller ivar | docker)
31m 48s
Test SISPA (latest-everything | --gff false | docker)
21m 11s
Run pipeline with test data (24.04.2 | test | docker)
30m 53s
Test parameters (24.04.2 | --variant_caller bcftools --consensus_caller ivar | docker)
29m 28s
Test SISPA (latest-everything | --genome 'NC_045512.2' | docker)
22m 16s
Run pipeline with test data (latest-everything | test | docker)
30m 36s
Test parameters (24.04.2 | --skip_fastp --skip_pangolin | docker)
30m 0s
Test parameters (24.04.2 | --skip_variants | docker)
11m 53s
Test parameters (24.04.2 | --skip_cutadapt --skip_snpeff | docker)
29m 5s
Test parameters (24.04.2 | --skip_kraken2 | docker)
31m 24s
Test nanopore (24.04.2 | --gff false --freyja_depthcutoff 1 | docker)
22m 0s
Test parameters (24.04.2 | --skip_assembly | docker)
24m 39s
Test nanopore (24.04.2 | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz --freyja_depthcutoff 1 | docker)
25m 11s
Test parameters (24.04.2 | --spades_mode corona | docker)
30m 36s
Test nanopore (24.04.2 | --input false --freyja_depthcutoff 1 | docker)
23m 51s
Test parameters (24.04.2 | --spades_mode metaviral | docker)
33m 56s
Test nanopore (24.04.2 | --min_barcode_reads 10000 | docker)
4m 13s
Test parameters (24.04.2 | --skip_plasmidid false --skip_asciigenome | docker)
32m 44s
Test nanopore (24.04.2 | --min_guppyplex_reads 10000 | docker)
9m 58s
Test parameters (24.04.2 | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz | docker)
30m 33s
Test nanopore (24.04.2 | --artic_minion_caller medaka --sequencing_summary false --fast5_dir false --freyja_depthcutoff 1 | docker)
40m 10s
Test parameters (24.04.2 | --bowtie2_index ./GCA_009858895.3_ASM985889v3_genomic.200409.bt2.index.tar.gz | docker)
30m 41s
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)
37m 45s
Test parameters (24.04.2 | --skip_noninternal_primers --threeprime_adapters | docker)
27m 48s
Test nanopore (latest-everything | --gff false --freyja_depthcutoff 1 | docker)
22m 4s
Test parameters (latest-everything | --consensus_caller ivar | docker)
31m 45s
Test nanopore (latest-everything | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz --freyja_depthcutoff 1 | docker)
25m 20s
Test parameters (latest-everything | --variant_caller bcftools --consensus_caller ivar | docker)
29m 22s
Test parameters (latest-everything | --skip_fastp --skip_pangolin | docker)
31m 40s
Test nanopore (latest-everything | --input false --freyja_depthcutoff 1 | docker)
24m 19s
Test parameters (latest-everything | --skip_variants | docker)
11m 16s
Test nanopore (latest-everything | --min_barcode_reads 10000 | docker)
4m 32s
Test parameters (latest-everything | --skip_cutadapt --skip_snpeff | docker)
28m 24s
Test nanopore (latest-everything | --min_guppyplex_reads 10000 | docker)
7m 6s
Test parameters (latest-everything | --skip_kraken2 | docker)
30m 34s
Test nanopore (latest-everything | --artic_minion_caller medaka --sequencing_summary false --fast5_dir false --freyja_depthcutoff 1 | docker)
38m 12s
Test parameters (latest-everything | --skip_assembly | docker)
24m 15s
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 2s
Test parameters (latest-everything | --spades_mode corona | docker)
29m 45s
Test parameters (latest-everything | --spades_mode metaviral | docker)
30m 13s
Test parameters (latest-everything | --skip_plasmidid false --skip_asciigenome | docker)
31m 45s
Test parameters (latest-everything | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz | docker)
32m 42s
Test parameters (latest-everything | --bowtie2_index ./GCA_009858895.3_ASM985889v3_genomic.200409.bt2.index.tar.gz | docker)
30m 51s
Test parameters (latest-everything | --skip_noninternal_primers --threeprime_adapters | docker)
28m 39s
20h 18m 54s