Skip to content
nf-core CI

Update nextclade & pangolin modules #1352

Sign in to view logs

Update nextclade & pangolin modules

Update nextclade & pangolin modules #1352

Run time

Learn about OS pricing on GitHub Actions
Job Run time
Run pipeline with test data (24.04.2 | test | docker)
29m 52s
Run pipeline with test data (24.04.2 | test | docker)
29m 52s
Test nanopore (24.04.2 | --gff false --freyja_depthcutoff 1 | docker)
17m 20s
Test nanopore (24.04.2 | --gff false --freyja_depthcutoff 1 | docker)
36m 14s
Run pipeline with test data (latest-everything | test | docker)
30m 11s
Run pipeline with test data (latest-everything | test | docker)
30m 11s
Test nanopore (24.04.2 | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz --freyja_depthcutoff 1 | docker)
17m 19s
Test nanopore (24.04.2 | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz --freyja_depthcutoff 1 | docker)
38m 28s
Test parameters (24.04.2 | --consensus_caller ivar | docker)
30m 37s
Test parameters (24.04.2 | --consensus_caller ivar | docker)
30m 37s
Test nanopore (24.04.2 | --input false --freyja_depthcutoff 1 | docker)
17m 18s
Test nanopore (24.04.2 | --input false --freyja_depthcutoff 1 | docker)
38m 56s
Test SISPA (24.04.2 | --gff false | docker)
20m 49s
Test SISPA (24.04.2 | --gff false | docker)
20m 49s
Test parameters (24.04.2 | --variant_caller bcftools --consensus_caller ivar | docker)
31m 19s
Test parameters (24.04.2 | --variant_caller bcftools --consensus_caller ivar | docker)
31m 19s
Test nanopore (24.04.2 | --min_barcode_reads 10000 | docker)
3m 59s
Test nanopore (24.04.2 | --min_barcode_reads 10000 | docker)
3m 59s
Test SISPA (24.04.2 | --genome 'NC_045512.2' | docker)
22m 13s
Test SISPA (24.04.2 | --genome 'NC_045512.2' | docker)
22m 13s
Test nanopore (24.04.2 | --min_guppyplex_reads 10000 | docker)
8m 34s
Test nanopore (24.04.2 | --min_guppyplex_reads 10000 | docker)
8m 34s
Test SISPA (latest-everything | --gff false | docker)
22m 30s
Test SISPA (latest-everything | --gff false | docker)
22m 30s
Test SISPA (latest-everything | --genome 'NC_045512.2' | docker)
21m 36s
Test SISPA (latest-everything | --genome 'NC_045512.2' | docker)
21m 36s
Test nanopore (24.04.2 | --artic_minion_caller medaka --sequencing_summary false --fast5_dir false --freyja_depthcutoff 1 | docker)
17m 18s
Test nanopore (24.04.2 | --artic_minion_caller medaka --sequencing_summary false --fast5_dir false --freyja_depthcutoff 1 | docker)
51m 53s
Test parameters (24.04.2 | --skip_fastp --skip_pangolin | docker)
31m 49s
Test parameters (24.04.2 | --skip_fastp --skip_pangolin | docker)
31m 49s
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)
17m 19s
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)
51m 57s
Test parameters (24.04.2 | --skip_variants | docker)
11m 6s
Test parameters (24.04.2 | --skip_variants | docker)
11m 6s
Test nanopore (latest-everything | --gff false --freyja_depthcutoff 1 | docker)
17m 19s
Test nanopore (latest-everything | --gff false --freyja_depthcutoff 1 | docker)
37m 31s
Test parameters (24.04.2 | --skip_cutadapt --skip_snpeff | docker)
30m 15s
Test parameters (24.04.2 | --skip_cutadapt --skip_snpeff | docker)
30m 15s
Test nanopore (latest-everything | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz --freyja_depthcutoff 1 | docker)
17m 1s
Test nanopore (latest-everything | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz --freyja_depthcutoff 1 | docker)
40m 23s
Test parameters (24.04.2 | --skip_kraken2 | docker)
31m 51s
Test parameters (24.04.2 | --skip_kraken2 | docker)
31m 51s
Test nanopore (latest-everything | --input false --freyja_depthcutoff 1 | docker)
17m 19s
Test nanopore (latest-everything | --input false --freyja_depthcutoff 1 | docker)
40m 52s
Test parameters (24.04.2 | --skip_assembly | docker)
24m 10s
Test parameters (24.04.2 | --skip_assembly | docker)
24m 10s
Test nanopore (latest-everything | --min_barcode_reads 10000 | docker)
6m 25s
Test nanopore (latest-everything | --min_barcode_reads 10000 | docker)
6m 25s
Test nanopore (latest-everything | --min_guppyplex_reads 10000 | docker)
7m 3s
Test nanopore (latest-everything | --min_guppyplex_reads 10000 | docker)
7m 3s
Test parameters (24.04.2 | --spades_mode corona | docker)
30m 9s
Test parameters (24.04.2 | --spades_mode corona | docker)
30m 9s
Test parameters (24.04.2 | --spades_mode metaviral | docker)
29m 42s
Test parameters (24.04.2 | --spades_mode metaviral | docker)
29m 42s
Test nanopore (latest-everything | --artic_minion_caller medaka --sequencing_summary false --fast5_dir false --freyja_depthcutoff 1 | docker)
17m 18s
Test nanopore (latest-everything | --artic_minion_caller medaka --sequencing_summary false --fast5_dir false --freyja_depthcutoff 1 | docker)
52m 26s
Test parameters (24.04.2 | --skip_plasmidid false --skip_asciigenome | docker)
54m 6s
Test parameters (24.04.2 | --skip_plasmidid false --skip_asciigenome | docker)
54m 6s
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)
17m 18s
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)
52m 54s
Test parameters (24.04.2 | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz | docker)
37m 58s
Test parameters (24.04.2 | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz | docker)
37m 58s
Test parameters (24.04.2 | --bowtie2_index ./GCA_009858895.3_ASM985889v3_genomic.200409.bt2.index.tar.gz | docker)
29m 23s
Test parameters (24.04.2 | --bowtie2_index ./GCA_009858895.3_ASM985889v3_genomic.200409.bt2.index.tar.gz | docker)
29m 23s
Test parameters (24.04.2 | --skip_noninternal_primers --threeprime_adapters | docker)
28m 55s
Test parameters (24.04.2 | --skip_noninternal_primers --threeprime_adapters | docker)
28m 55s
Test parameters (latest-everything | --consensus_caller ivar | docker)
30m 16s
Test parameters (latest-everything | --consensus_caller ivar | docker)
30m 16s
Test parameters (latest-everything | --variant_caller bcftools --consensus_caller ivar | docker)
28m 54s
Test parameters (latest-everything | --variant_caller bcftools --consensus_caller ivar | docker)
28m 54s
Test parameters (latest-everything | --skip_fastp --skip_pangolin | docker)
29m 10s
Test parameters (latest-everything | --skip_fastp --skip_pangolin | docker)
29m 10s
Test parameters (latest-everything | --skip_variants | docker)
15m 12s
Test parameters (latest-everything | --skip_variants | docker)
15m 12s
Test parameters (latest-everything | --skip_cutadapt --skip_snpeff | docker)
36m 3s
Test parameters (latest-everything | --skip_cutadapt --skip_snpeff | docker)
36m 3s
Test parameters (latest-everything | --skip_kraken2 | docker)
33m 23s
Test parameters (latest-everything | --skip_kraken2 | docker)
33m 23s
Test parameters (latest-everything | --skip_assembly | docker)
24m 4s
Test parameters (latest-everything | --skip_assembly | docker)
24m 4s
Test parameters (latest-everything | --spades_mode corona | docker)
32m 1s
Test parameters (latest-everything | --spades_mode corona | docker)
32m 1s
Test parameters (latest-everything | --spades_mode metaviral | docker)
32m 5s
Test parameters (latest-everything | --spades_mode metaviral | docker)
32m 5s
Test parameters (latest-everything | --skip_plasmidid false --skip_asciigenome | docker)
45m 50s
Test parameters (latest-everything | --skip_plasmidid false --skip_asciigenome | docker)
45m 50s
Test parameters (latest-everything | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz | docker)
37m 32s
Test parameters (latest-everything | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz | docker)
37m 32s
Test parameters (latest-everything | --bowtie2_index ./GCA_009858895.3_ASM985889v3_genomic.200409.bt2.index.tar.gz | docker)
32m 36s
Test parameters (latest-everything | --bowtie2_index ./GCA_009858895.3_ASM985889v3_genomic.200409.bt2.index.tar.gz | docker)
32m 36s
Test parameters (latest-everything | --skip_noninternal_primers --threeprime_adapters | docker)
28m 55s
Test parameters (latest-everything | --skip_noninternal_primers --threeprime_adapters | docker)
28m 55s
1d 18h 55m 29s