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Update nextclade & pangolin modules #1351

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Update nextclade & pangolin modules

Update nextclade & pangolin modules #1351

Run time

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Job Run time
Test SISPA (24.04.2 | --gff false | docker)
19m 18s
Test SISPA (24.04.2 | --gff false | docker)
21m 56s
Test SISPA (24.04.2 | --gff false | docker)
21m 56s
Test SISPA (24.04.2 | --genome 'NC_045512.2' | docker)
19m 24s
Test SISPA (24.04.2 | --genome 'NC_045512.2' | docker)
22m 10s
Test SISPA (24.04.2 | --genome 'NC_045512.2' | docker)
22m 10s
Test parameters (24.04.2 | --consensus_caller ivar | docker)
15m 31s
Test parameters (24.04.2 | --consensus_caller ivar | docker)
31m 37s
Test parameters (24.04.2 | --consensus_caller ivar | docker)
31m 37s
Run pipeline with test data (24.04.2 | test | docker)
29m 6s
Run pipeline with test data (24.04.2 | test | docker)
3m 11s
Run pipeline with test data (24.04.2 | test | docker)
30m 28s
Test SISPA (latest-everything | --gff false | docker)
19m 9s
Test SISPA (latest-everything | --gff false | docker)
20m 53s
Test SISPA (latest-everything | --gff false | docker)
20m 53s
Test parameters (24.04.2 | --variant_caller bcftools --consensus_caller ivar | docker)
15m 14s
Test parameters (24.04.2 | --variant_caller bcftools --consensus_caller ivar | docker)
28m 32s
Test parameters (24.04.2 | --variant_caller bcftools --consensus_caller ivar | docker)
28m 32s
Run pipeline with test data (latest-everything | test | docker)
29m 5s
Run pipeline with test data (latest-everything | test | docker)
3m 22s
Run pipeline with test data (latest-everything | test | docker)
33m 25s
Test parameters (24.04.2 | --skip_fastp --skip_pangolin | docker)
15m 31s
Test parameters (24.04.2 | --skip_fastp --skip_pangolin | docker)
30m 7s
Test parameters (24.04.2 | --skip_fastp --skip_pangolin | docker)
30m 7s
Test SISPA (latest-everything | --genome 'NC_045512.2' | docker)
19m 23s
Test SISPA (latest-everything | --genome 'NC_045512.2' | docker)
22m 49s
Test SISPA (latest-everything | --genome 'NC_045512.2' | docker)
22m 49s
Test parameters (24.04.2 | --skip_variants | docker)
13m 14s
Test parameters (24.04.2 | --skip_variants | docker)
13m 14s
Test parameters (24.04.2 | --skip_variants | docker)
13m 14s
Test parameters (24.04.2 | --skip_cutadapt --skip_snpeff | docker)
15m 31s
Test parameters (24.04.2 | --skip_cutadapt --skip_snpeff | docker)
30m 9s
Test parameters (24.04.2 | --skip_cutadapt --skip_snpeff | docker)
30m 9s
Test nanopore (24.04.2 | --gff false --freyja_depthcutoff 1 | docker)
10m 56s
Test nanopore (24.04.2 | --gff false --freyja_depthcutoff 1 | docker)
36m 7s
Test nanopore (24.04.2 | --gff false --freyja_depthcutoff 1 | docker)
36m 7s
Test parameters (24.04.2 | --skip_kraken2 | docker)
15m 30s
Test parameters (24.04.2 | --skip_kraken2 | docker)
31m 17s
Test parameters (24.04.2 | --skip_kraken2 | docker)
31m 17s
Test nanopore (24.04.2 | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz --freyja_depthcutoff 1 | docker)
11m 12s
Test nanopore (24.04.2 | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz --freyja_depthcutoff 1 | docker)
40m 8s
Test nanopore (24.04.2 | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz --freyja_depthcutoff 1 | docker)
40m 8s
Test parameters (24.04.2 | --skip_assembly | docker)
15m 31s
Test parameters (24.04.2 | --skip_assembly | docker)
25m 39s
Test parameters (24.04.2 | --skip_assembly | docker)
25m 39s
Test nanopore (24.04.2 | --input false --freyja_depthcutoff 1 | docker)
10m 56s
Test nanopore (24.04.2 | --input false --freyja_depthcutoff 1 | docker)
38m 5s
Test nanopore (24.04.2 | --input false --freyja_depthcutoff 1 | docker)
38m 5s
Test parameters (24.04.2 | --spades_mode corona | docker)
15m 31s
Test parameters (24.04.2 | --spades_mode corona | docker)
30m 3s
Test parameters (24.04.2 | --spades_mode corona | docker)
30m 3s
Test parameters (24.04.2 | --spades_mode metaviral | docker)
15m 30s
Test parameters (24.04.2 | --spades_mode metaviral | docker)
30m 44s
Test parameters (24.04.2 | --spades_mode metaviral | docker)
30m 44s
Test nanopore (24.04.2 | --min_barcode_reads 10000 | docker)
5m 15s
Test nanopore (24.04.2 | --min_barcode_reads 10000 | docker)
5m 15s
Test nanopore (24.04.2 | --min_barcode_reads 10000 | docker)
5m 15s
Test parameters (24.04.2 | --skip_plasmidid false --skip_asciigenome | docker)
15m 30s
Test parameters (24.04.2 | --skip_plasmidid false --skip_asciigenome | docker)
33m 27s
Test parameters (24.04.2 | --skip_plasmidid false --skip_asciigenome | docker)
33m 27s
Test nanopore (24.04.2 | --min_guppyplex_reads 10000 | docker)
7m 18s
Test nanopore (24.04.2 | --min_guppyplex_reads 10000 | docker)
7m 18s
Test nanopore (24.04.2 | --min_guppyplex_reads 10000 | docker)
7m 18s
Test parameters (24.04.2 | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz | docker)
15m 31s
Test parameters (24.04.2 | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz | docker)
31m 35s
Test parameters (24.04.2 | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz | docker)
31m 35s
Test nanopore (24.04.2 | --artic_minion_caller medaka --sequencing_summary false --fast5_dir false --freyja_depthcutoff 1 | docker)
11m 11s
Test nanopore (24.04.2 | --artic_minion_caller medaka --sequencing_summary false --fast5_dir false --freyja_depthcutoff 1 | docker)
51m 52s
Test nanopore (24.04.2 | --artic_minion_caller medaka --sequencing_summary false --fast5_dir false --freyja_depthcutoff 1 | docker)
51m 52s
Test parameters (24.04.2 | --bowtie2_index ./GCA_009858895.3_ASM985889v3_genomic.200409.bt2.index.tar.gz | docker)
15m 31s
Test parameters (24.04.2 | --bowtie2_index ./GCA_009858895.3_ASM985889v3_genomic.200409.bt2.index.tar.gz | docker)
31m 1s
Test parameters (24.04.2 | --bowtie2_index ./GCA_009858895.3_ASM985889v3_genomic.200409.bt2.index.tar.gz | docker)
31m 1s
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)
11m 10s
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)
52m 36s
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)
52m 36s
Test parameters (24.04.2 | --skip_noninternal_primers --threeprime_adapters | docker)
15m 31s
Test parameters (24.04.2 | --skip_noninternal_primers --threeprime_adapters | docker)
27m 42s
Test parameters (24.04.2 | --skip_noninternal_primers --threeprime_adapters | docker)
27m 42s
Test nanopore (latest-everything | --gff false --freyja_depthcutoff 1 | docker)
11m 11s
Test nanopore (latest-everything | --gff false --freyja_depthcutoff 1 | docker)
37m 46s
Test nanopore (latest-everything | --gff false --freyja_depthcutoff 1 | docker)
37m 46s
Test parameters (latest-everything | --consensus_caller ivar | docker)
15m 29s
Test parameters (latest-everything | --consensus_caller ivar | docker)
29m 14s
Test parameters (latest-everything | --consensus_caller ivar | docker)
29m 14s
Test nanopore (latest-everything | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz --freyja_depthcutoff 1 | docker)
11m 11s
Test nanopore (latest-everything | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz --freyja_depthcutoff 1 | docker)
38m 5s
Test nanopore (latest-everything | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz --freyja_depthcutoff 1 | docker)
38m 5s
Test parameters (latest-everything | --variant_caller bcftools --consensus_caller ivar | docker)
15m 31s
Test parameters (latest-everything | --variant_caller bcftools --consensus_caller ivar | docker)
31m 8s
Test parameters (latest-everything | --variant_caller bcftools --consensus_caller ivar | docker)
31m 8s
Test nanopore (latest-everything | --input false --freyja_depthcutoff 1 | docker)
11m 6s
Test nanopore (latest-everything | --input false --freyja_depthcutoff 1 | docker)
39m 31s
Test nanopore (latest-everything | --input false --freyja_depthcutoff 1 | docker)
39m 31s
Test parameters (latest-everything | --skip_fastp --skip_pangolin | docker)
15m 33s
Test parameters (latest-everything | --skip_fastp --skip_pangolin | docker)
32m 19s
Test parameters (latest-everything | --skip_fastp --skip_pangolin | docker)
32m 19s
Test nanopore (latest-everything | --min_barcode_reads 10000 | docker)
5m 11s
Test nanopore (latest-everything | --min_barcode_reads 10000 | docker)
5m 11s
Test nanopore (latest-everything | --min_barcode_reads 10000 | docker)
5m 11s
Test parameters (latest-everything | --skip_variants | docker)
12m 18s
Test parameters (latest-everything | --skip_variants | docker)
12m 18s
Test parameters (latest-everything | --skip_variants | docker)
12m 18s
Test nanopore (latest-everything | --min_guppyplex_reads 10000 | docker)
8m 23s
Test nanopore (latest-everything | --min_guppyplex_reads 10000 | docker)
8m 23s
Test nanopore (latest-everything | --min_guppyplex_reads 10000 | docker)
8m 23s
Test parameters (latest-everything | --skip_cutadapt --skip_snpeff | docker)
15m 30s
Test parameters (latest-everything | --skip_cutadapt --skip_snpeff | docker)
30m 26s
Test parameters (latest-everything | --skip_cutadapt --skip_snpeff | docker)
30m 26s
Test nanopore (latest-everything | --artic_minion_caller medaka --sequencing_summary false --fast5_dir false --freyja_depthcutoff 1 | docker)
11m 10s
Test nanopore (latest-everything | --artic_minion_caller medaka --sequencing_summary false --fast5_dir false --freyja_depthcutoff 1 | docker)
51m 39s
Test nanopore (latest-everything | --artic_minion_caller medaka --sequencing_summary false --fast5_dir false --freyja_depthcutoff 1 | docker)
51m 39s
Test parameters (latest-everything | --skip_kraken2 | docker)
15m 28s
Test parameters (latest-everything | --skip_kraken2 | docker)
30m 21s
Test parameters (latest-everything | --skip_kraken2 | docker)
30m 21s
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)
11m 11s
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)
53m 57s
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)
53m 57s
Test parameters (latest-everything | --skip_assembly | docker)
15m 30s
Test parameters (latest-everything | --skip_assembly | docker)
25m 13s
Test parameters (latest-everything | --skip_assembly | docker)
25m 13s
Test parameters (latest-everything | --spades_mode corona | docker)
15m 28s
Test parameters (latest-everything | --spades_mode corona | docker)
32m 0s
Test parameters (latest-everything | --spades_mode corona | docker)
32m 0s
Test parameters (latest-everything | --spades_mode metaviral | docker)
15m 30s
Test parameters (latest-everything | --spades_mode metaviral | docker)
29m 58s
Test parameters (latest-everything | --spades_mode metaviral | docker)
29m 58s
Test parameters (latest-everything | --skip_plasmidid false --skip_asciigenome | docker)
15m 31s
Test parameters (latest-everything | --skip_plasmidid false --skip_asciigenome | docker)
31m 42s
Test parameters (latest-everything | --skip_plasmidid false --skip_asciigenome | docker)
31m 42s
Test parameters (latest-everything | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz | docker)
15m 30s
Test parameters (latest-everything | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz | docker)
31m 29s
Test parameters (latest-everything | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz | docker)
31m 29s
Test parameters (latest-everything | --bowtie2_index ./GCA_009858895.3_ASM985889v3_genomic.200409.bt2.index.tar.gz | docker)
15m 30s
Test parameters (latest-everything | --bowtie2_index ./GCA_009858895.3_ASM985889v3_genomic.200409.bt2.index.tar.gz | docker)
29m 55s
Test parameters (latest-everything | --bowtie2_index ./GCA_009858895.3_ASM985889v3_genomic.200409.bt2.index.tar.gz | docker)
29m 55s
Test parameters (latest-everything | --skip_noninternal_primers --threeprime_adapters | docker)
15m 30s
Test parameters (latest-everything | --skip_noninternal_primers --threeprime_adapters | docker)
29m 49s
Test parameters (latest-everything | --skip_noninternal_primers --threeprime_adapters | docker)
29m 49s
2d 7h 49m 56s