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Update nextclade & pangolin modules #1350

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Update nextclade & pangolin modules

Update nextclade & pangolin modules #1350

Run time

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Job Run time
Run pipeline with test data (24.04.2 | test | docker)
6m 39s
Test nanopore (24.04.2 | --gff false --freyja_depthcutoff 1 | docker)
6m 37s
Run pipeline with test data (latest-everything | test | docker)
6m 40s
Test nanopore (24.04.2 | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz --freyja_depthcutoff 1 | docker)
6m 38s
Test parameters (24.04.2 | --consensus_caller ivar | docker)
6m 37s
Test nanopore (24.04.2 | --input false --freyja_depthcutoff 1 | docker)
6m 39s
Test SISPA (24.04.2 | --gff false | docker)
6m 36s
Test nanopore (24.04.2 | --min_barcode_reads 10000 | docker)
4m 39s
Test parameters (24.04.2 | --variant_caller bcftools --consensus_caller ivar | docker)
6m 36s
Test nanopore (24.04.2 | --min_guppyplex_reads 10000 | docker)
6m 40s
Test parameters (24.04.2 | --skip_fastp --skip_pangolin | docker)
6m 38s
Test SISPA (24.04.2 | --genome 'NC_045512.2' | docker)
6m 37s
Test parameters (24.04.2 | --skip_variants | docker)
6m 39s
Test nanopore (24.04.2 | --artic_minion_caller medaka --sequencing_summary false --fast5_dir false --freyja_depthcutoff 1 | docker)
6m 40s
Test SISPA (latest-everything | --gff false | docker)
6m 35s
Test parameters (24.04.2 | --skip_cutadapt --skip_snpeff | docker)
6m 37s
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)
6m 40s
Test SISPA (latest-everything | --genome 'NC_045512.2' | docker)
6m 35s
Test nanopore (latest-everything | --gff false --freyja_depthcutoff 1 | docker)
6m 36s
Test parameters (24.04.2 | --skip_kraken2 | docker)
6m 38s
Test nanopore (latest-everything | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz --freyja_depthcutoff 1 | docker)
6m 39s
Test parameters (24.04.2 | --skip_assembly | docker)
6m 39s
Test nanopore (latest-everything | --input false --freyja_depthcutoff 1 | docker)
6m 38s
Test parameters (24.04.2 | --spades_mode corona | docker)
6m 37s
Test nanopore (latest-everything | --min_barcode_reads 10000 | docker)
5m 41s
Test parameters (24.04.2 | --spades_mode metaviral | docker)
6m 38s
Test nanopore (latest-everything | --min_guppyplex_reads 10000 | docker)
6m 39s
Test parameters (24.04.2 | --skip_plasmidid false --skip_asciigenome | docker)
6m 37s
Test parameters (24.04.2 | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz | docker)
6m 36s
Test parameters (24.04.2 | --bowtie2_index ./GCA_009858895.3_ASM985889v3_genomic.200409.bt2.index.tar.gz | docker)
6m 41s
Test nanopore (latest-everything | --artic_minion_caller medaka --sequencing_summary false --fast5_dir false --freyja_depthcutoff 1 | docker)
6m 40s
Test parameters (24.04.2 | --skip_noninternal_primers --threeprime_adapters | docker)
6m 38s
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)
6m 36s
Test parameters (latest-everything | --consensus_caller ivar | docker)
6m 34s
Test parameters (latest-everything | --variant_caller bcftools --consensus_caller ivar | docker)
6m 37s
Test parameters (latest-everything | --skip_fastp --skip_pangolin | docker)
6m 41s
Test parameters (latest-everything | --skip_variants | docker)
6m 36s
Test parameters (latest-everything | --skip_cutadapt --skip_snpeff | docker)
6m 37s
Test parameters (latest-everything | --skip_kraken2 | docker)
6m 36s
Test parameters (latest-everything | --skip_assembly | docker)
6m 36s
Test parameters (latest-everything | --spades_mode corona | docker)
6m 35s
Test parameters (latest-everything | --spades_mode metaviral | docker)
6m 37s
Test parameters (latest-everything | --skip_plasmidid false --skip_asciigenome | docker)
6m 37s
Test parameters (latest-everything | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz | docker)
6m 35s
Test parameters (latest-everything | --bowtie2_index ./GCA_009858895.3_ASM985889v3_genomic.200409.bt2.index.tar.gz | docker)
6m 41s
Test parameters (latest-everything | --skip_noninternal_primers --threeprime_adapters | docker)
6m 36s
5h 1m 53s