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Merge pull request #444 from nf-core/nf-core-template-merge-3.0.2 #1345

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Merge pull request #444 from nf-core/nf-core-template-merge-3.0.2

Merge pull request #444 from nf-core/nf-core-template-merge-3.0.2 #1345

Run time

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Job Run time
Run pipeline with test data (24.04.2 | test | docker)
33m 20s
Test SISPA (24.04.2 | --gff false | docker)
20m 40s
Run pipeline with test data (latest-everything | test | docker)
31m 58s
Test parameters (24.04.2 | --consensus_caller ivar | docker)
8m 33s
Test SISPA (24.04.2 | --genome 'NC_045512.2' | docker)
22m 2s
Test parameters (24.04.2 | --variant_caller bcftools --consensus_caller ivar | docker)
8m 30s
Test SISPA (latest-everything | --gff false | docker)
20m 31s
Test parameters (24.04.2 | --skip_fastp --skip_pangolin | docker)
8m 33s
Test nanopore (24.04.2 | --gff false --freyja_depthcutoff 1 | docker)
38m 11s
Test SISPA (latest-everything | --genome 'NC_045512.2' | docker)
21m 58s
Test parameters (24.04.2 | --skip_variants | docker)
8m 33s
Test nanopore (24.04.2 | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz --freyja_depthcutoff 1 | docker)
38m 35s
Test parameters (24.04.2 | --skip_cutadapt --skip_snpeff | docker)
8m 33s
Test nanopore (24.04.2 | --input false --freyja_depthcutoff 1 | docker)
1h 5m 59s
Test parameters (24.04.2 | --skip_kraken2 | docker)
8m 33s
Test nanopore (24.04.2 | --min_barcode_reads 10000 | docker)
6m 5s
Test nanopore (24.04.2 | --min_guppyplex_reads 10000 | docker)
1h 27m 49s
Test parameters (24.04.2 | --skip_assembly | docker)
8m 16s
Test nanopore (24.04.2 | --artic_minion_caller medaka --sequencing_summary false --fast5_dir false --freyja_depthcutoff 1 | docker)
50m 53s
Test parameters (24.04.2 | --spades_mode corona | docker)
8m 33s
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 20s
Test parameters (24.04.2 | --spades_mode metaviral | docker)
8m 32s
Test nanopore (latest-everything | --gff false --freyja_depthcutoff 1 | docker)
37m 43s
Test parameters (24.04.2 | --skip_plasmidid false --skip_asciigenome | docker)
8m 34s
Test nanopore (latest-everything | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz --freyja_depthcutoff 1 | docker)
43m 46s
Test parameters (24.04.2 | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz | docker)
8m 34s
Test nanopore (latest-everything | --input false --freyja_depthcutoff 1 | docker)
40m 55s
Test parameters (24.04.2 | --bowtie2_index ./GCA_009858895.3_ASM985889v3_genomic.200409.bt2.index.tar.gz | docker)
8m 34s
Test nanopore (latest-everything | --min_barcode_reads 10000 | docker)
4m 1s
Test parameters (latest-everything | --consensus_caller ivar | docker)
8m 31s
Test nanopore (latest-everything | --min_guppyplex_reads 10000 | docker)
7m 38s
Test parameters (latest-everything | --variant_caller bcftools --consensus_caller ivar | docker)
8m 32s
Test nanopore (latest-everything | --artic_minion_caller medaka --sequencing_summary false --fast5_dir false --freyja_depthcutoff 1 | docker)
53m 15s
Test parameters (latest-everything | --skip_fastp --skip_pangolin | docker)
8m 32s
Test parameters (latest-everything | --skip_variants | docker)
8m 31s
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 22s
Test parameters (latest-everything | --skip_cutadapt --skip_snpeff | docker)
8m 31s
Test parameters (latest-everything | --skip_kraken2 | docker)
8m 32s
Test parameters (latest-everything | --skip_assembly | docker)
8m 32s
Test parameters (latest-everything | --spades_mode corona | docker)
8m 31s
Test parameters (latest-everything | --spades_mode metaviral | docker)
8m 31s
Test parameters (latest-everything | --skip_plasmidid false --skip_asciigenome | docker)
8m 32s
Test parameters (latest-everything | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz | docker)
8m 34s
Test parameters (latest-everything | --bowtie2_index ./GCA_009858895.3_ASM985889v3_genomic.200409.bt2.index.tar.gz | docker)
8m 32s
15h 34m 40s