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Changed Cutadapt to use nf-core modules #1347

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Changed Cutadapt to use nf-core modules

Changed Cutadapt to use nf-core modules #1347

Run time

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Job Run time
Run pipeline with test data (24.04.2 | test | docker)
31m 44s
Run pipeline with test data (24.04.2 | test | docker)
31m 44s
Run pipeline with test data (latest-everything | test | docker)
29m 58s
Run pipeline with test data (latest-everything | test | docker)
29m 58s
Test parameters (24.04.2 | --consensus_caller ivar | docker)
6m 52s
Test parameters (24.04.2 | --consensus_caller ivar | docker)
6m 52s
Test nanopore (24.04.2 | --gff false --freyja_depthcutoff 1 | docker)
35m 4s
Test nanopore (24.04.2 | --gff false --freyja_depthcutoff 1 | docker)
35m 4s
Test parameters (24.04.2 | --variant_caller bcftools --consensus_caller ivar | docker)
5m 58s
Test parameters (24.04.2 | --variant_caller bcftools --consensus_caller ivar | docker)
5m 58s
Test SISPA (24.04.2 | --gff false | docker)
20m 49s
Test SISPA (24.04.2 | --gff false | docker)
20m 49s
Test nanopore (24.04.2 | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz --freyja_depthcutoff 1 | docker)
39m 21s
Test nanopore (24.04.2 | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz --freyja_depthcutoff 1 | docker)
39m 21s
Test parameters (24.04.2 | --skip_fastp --skip_pangolin | docker)
5m 55s
Test parameters (24.04.2 | --skip_fastp --skip_pangolin | docker)
5m 57s
Test SISPA (24.04.2 | --genome 'NC_045512.2' | docker)
21m 47s
Test SISPA (24.04.2 | --genome 'NC_045512.2' | docker)
21m 47s
Test nanopore (24.04.2 | --input false --freyja_depthcutoff 1 | docker)
38m 17s
Test nanopore (24.04.2 | --input false --freyja_depthcutoff 1 | docker)
38m 17s
Test parameters (24.04.2 | --skip_variants | docker)
5m 59s
Test parameters (24.04.2 | --skip_variants | docker)
5m 59s
Test SISPA (latest-everything | --gff false | docker)
22m 34s
Test SISPA (latest-everything | --gff false | docker)
22m 34s
Test nanopore (24.04.2 | --min_barcode_reads 10000 | docker)
3m 54s
Test nanopore (24.04.2 | --min_barcode_reads 10000 | docker)
3m 54s
Test parameters (24.04.2 | --skip_cutadapt --skip_snpeff | docker)
6m 27s
Test parameters (24.04.2 | --skip_cutadapt --skip_snpeff | docker)
6m 27s
Test SISPA (latest-everything | --genome 'NC_045512.2' | docker)
24m 13s
Test SISPA (latest-everything | --genome 'NC_045512.2' | docker)
24m 13s
Test nanopore (24.04.2 | --min_guppyplex_reads 10000 | docker)
6m 45s
Test nanopore (24.04.2 | --min_guppyplex_reads 10000 | docker)
6m 45s
Test parameters (24.04.2 | --skip_kraken2 | docker)
6m 2s
Test parameters (24.04.2 | --skip_kraken2 | docker)
6m 2s
Test nanopore (24.04.2 | --artic_minion_caller medaka --sequencing_summary false --fast5_dir false --freyja_depthcutoff 1 | docker)
49m 41s
Test nanopore (24.04.2 | --artic_minion_caller medaka --sequencing_summary false --fast5_dir false --freyja_depthcutoff 1 | docker)
49m 41s
Test parameters (24.04.2 | --skip_assembly | docker)
6m 52s
Test parameters (24.04.2 | --skip_assembly | docker)
6m 52s
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 27s
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 27s
Test parameters (24.04.2 | --spades_mode corona | docker)
6m 1s
Test parameters (24.04.2 | --spades_mode corona | docker)
6m 1s
Test nanopore (latest-everything | --gff false --freyja_depthcutoff 1 | docker)
35m 27s
Test nanopore (latest-everything | --gff false --freyja_depthcutoff 1 | docker)
35m 27s
Test parameters (24.04.2 | --spades_mode metaviral | docker)
6m 1s
Test parameters (24.04.2 | --spades_mode metaviral | docker)
6m 1s
Test nanopore (latest-everything | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz --freyja_depthcutoff 1 | docker)
38m 16s
Test nanopore (latest-everything | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz --freyja_depthcutoff 1 | docker)
38m 16s
Test parameters (24.04.2 | --skip_plasmidid false --skip_asciigenome | docker)
6m 2s
Test parameters (24.04.2 | --skip_plasmidid false --skip_asciigenome | docker)
6m 2s
Test nanopore (latest-everything | --input false --freyja_depthcutoff 1 | docker)
39m 45s
Test nanopore (latest-everything | --input false --freyja_depthcutoff 1 | docker)
39m 45s
Test nanopore (latest-everything | --min_barcode_reads 10000 | docker)
3m 52s
Test nanopore (latest-everything | --min_barcode_reads 10000 | docker)
3m 52s
Test parameters (24.04.2 | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz | docker)
6m 53s
Test parameters (24.04.2 | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz | docker)
6m 53s
Test parameters (24.04.2 | --bowtie2_index ./GCA_009858895.3_ASM985889v3_genomic.200409.bt2.index.tar.gz | docker)
6m 47s
Test parameters (24.04.2 | --bowtie2_index ./GCA_009858895.3_ASM985889v3_genomic.200409.bt2.index.tar.gz | docker)
6m 47s
Test parameters (24.04.2 | --skip_noninternal_primers --threeprime_adapters | docker)
6m 4s
Test parameters (24.04.2 | --skip_noninternal_primers --threeprime_adapters | docker)
6m 4s
Test nanopore (latest-everything | --min_guppyplex_reads 10000 | docker)
6m 27s
Test nanopore (latest-everything | --min_guppyplex_reads 10000 | docker)
6m 27s
Test parameters (latest-everything | --consensus_caller ivar | docker)
4m 9s
Test parameters (latest-everything | --consensus_caller ivar | docker)
4m 9s
Test nanopore (latest-everything | --artic_minion_caller medaka --sequencing_summary false --fast5_dir false --freyja_depthcutoff 1 | docker)
51m 57s
Test nanopore (latest-everything | --artic_minion_caller medaka --sequencing_summary false --fast5_dir false --freyja_depthcutoff 1 | docker)
51m 57s
Test parameters (latest-everything | --variant_caller bcftools --consensus_caller ivar | docker)
5m 49s
Test parameters (latest-everything | --variant_caller bcftools --consensus_caller ivar | docker)
5m 49s
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 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 11s
Test parameters (latest-everything | --skip_fastp --skip_pangolin | docker)
5m 54s
Test parameters (latest-everything | --skip_fastp --skip_pangolin | docker)
5m 54s
Test parameters (latest-everything | --skip_variants | docker)
5m 53s
Test parameters (latest-everything | --skip_variants | docker)
5m 53s
Test parameters (latest-everything | --skip_cutadapt --skip_snpeff | docker)
5m 48s
Test parameters (latest-everything | --skip_cutadapt --skip_snpeff | docker)
5m 48s
Test parameters (latest-everything | --skip_kraken2 | docker)
4m 38s
Test parameters (latest-everything | --skip_kraken2 | docker)
4m 38s
Test parameters (latest-everything | --skip_assembly | docker)
5m 26s
Test parameters (latest-everything | --skip_assembly | docker)
5m 26s
Test parameters (latest-everything | --spades_mode corona | docker)
5m 26s
Test parameters (latest-everything | --spades_mode corona | docker)
5m 26s
Test parameters (latest-everything | --spades_mode metaviral | docker)
4m 19s
Test parameters (latest-everything | --spades_mode metaviral | docker)
4m 19s
Test parameters (latest-everything | --skip_plasmidid false --skip_asciigenome | docker)
5m 59s
Test parameters (latest-everything | --skip_plasmidid false --skip_asciigenome | docker)
5m 59s
Test parameters (latest-everything | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz | docker)
5m 59s
Test parameters (latest-everything | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz | docker)
5m 59s
Test parameters (latest-everything | --bowtie2_index ./GCA_009858895.3_ASM985889v3_genomic.200409.bt2.index.tar.gz | docker)
5m 52s
Test parameters (latest-everything | --bowtie2_index ./GCA_009858895.3_ASM985889v3_genomic.200409.bt2.index.tar.gz | docker)
5m 52s
Test parameters (latest-everything | --skip_noninternal_primers --threeprime_adapters | docker)
5m 54s
Test parameters (latest-everything | --skip_noninternal_primers --threeprime_adapters | docker)
5m 54s
1d 1h 14m 58s