Switch CI to self hosted runners and update minimal nextflow version #1443
ci.yml
on: pull_request
Matrix: test
Matrix: test_nanopore
Matrix: test_parameters
Matrix: test_sispa
Annotations
92 warnings
|
Test nanopore (24.10.5 | --min_barcode_reads 10000 | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Test nanopore (24.10.5 | --min_barcode_reads 10000 | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
Test nanopore (latest-everything | --min_barcode_reads 10000 | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Test nanopore (latest-everything | --min_barcode_reads 10000 | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
Test nanopore (latest-everything | --min_guppyplex_reads 10000 | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Test nanopore (latest-everything | --min_guppyplex_reads 10000 | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
Test nanopore (24.10.5 | --min_guppyplex_reads 10000 | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Test nanopore (24.10.5 | --min_guppyplex_reads 10000 | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (latest-everything | --skip_variants | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (latest-everything | --skip_variants | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (24.10.5 | --skip_variants | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (24.10.5 | --skip_variants | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
Test SISPA (latest-everything | --gff false | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Test SISPA (latest-everything | --gff false | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
Test nanopore (24.10.5 | --gff false --freyja_depthcutoff 1 | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Test nanopore (24.10.5 | --gff false --freyja_depthcutoff 1 | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
Test nanopore (latest-everything | --gff false --freyja_depthcutoff 1 | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Test nanopore (latest-everything | --gff false --freyja_depthcutoff 1 | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
Test SISPA (24.10.5 | --genome 'NC_045512.2' | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Test SISPA (24.10.5 | --genome 'NC_045512.2' | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
Test SISPA (24.10.5 | --gff false | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Test SISPA (24.10.5 | --gff false | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
10000
|
Test SISPA (latest-everything | --genome 'NC_045512.2' | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Test SISPA (latest-everything | --genome 'NC_045512.2' | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
Test nanopore (latest-everything | --input false --freyja_depthcutoff 1 | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Test nanopore (latest-everything | --input false --freyja_depthcutoff 1 | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
Test nanopore (24.10.5 | --input false --freyja_depthcutoff 1 | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Test nanopore (24.10.5 | --input false --freyja_depthcutoff 1 | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (latest-everything | --skip_assembly | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (latest-everything | --skip_assembly | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (24.10.5 | --skip_assembly | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (24.10.5 | --skip_assembly | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
Test nanopore (latest-everything | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz --freyja_depthcutoff 1 | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Test nanopore (latest-everything | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz --freyja_depthcutoff 1 | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
Test nanopore (24.10.5 | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz --freyja_depthcutoff 1 | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Test nanopore (24.10.5 | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz --freyja_depthcutoff 1 | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (24.10.5 | --skip_noninternal_primers --threeprime_adapters | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (24.10.5 | --skip_noninternal_primers --threeprime_adapters | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (latest-everything | --skip_noninternal_primers --threeprime_adapters | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (latest-everything | --skip_noninternal_primers --threeprime_adapters | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (latest-everything | --skip_fastp --skip_pangolin | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (latest-everything | --skip_fastp --skip_pangolin | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (24.10.5 | --spades_mode metaviral | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (24.10.5 | --spades_mode metaviral | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (latest-everything | --spades_mode corona | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (latest-everything | --spades_mode corona | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (latest-everything | --skip_kraken2 | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (latest-everything | --skip_kraken2 | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
Test nanopore (24.10.5 | --artic_minion_caller medaka --sequencing_summary false --fast5_dir false --artic_minion_medaka_model ./r941_min_high_g360_model.hdf5 --freyja_depthcutoff 1 | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Test nanopore (24.10.5 | --artic_minion_caller medaka --sequencing_summary false --fast5_dir false --artic_minion_medaka_model ./r941_min_high_g360_model.hdf5 --freyja_depthcutoff 1 | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (latest-everything | --consensus_caller ivar | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (latest-everything | --consensus_caller ivar | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (latest-everything | --skip_cutadapt --skip_snpeff | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (latest-everything | --skip_cutadapt --skip_snpeff | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (24.10.5 | --variant_caller bcftools --consensus_caller ivar | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (24.10.5 | --variant_caller bcftools --consensus_caller ivar | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (latest-everything | --variant_caller bcftools --consensus_caller ivar | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (latest-everything | --variant_caller bcftools --consensus_caller ivar | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (latest-everything | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (latest-everything | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
Run pipeline with test data (latest-everything | test | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Run pipeline with test data (latest-everything | test | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (latest-everything | --bowtie2_index ./GCA_009858895.3_ASM985889v3_genomic.200409.bt2.index.tar.gz | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (latest-everything | --bowtie2_index ./GCA_009858895.3_ASM985889v3_genomic.200409.bt2.index.tar.gz | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (24.10.5 | --skip_kraken2 | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (24.10.5 | --skip_kraken2 | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (24.10.5 | --skip_cutadapt --skip_snpeff | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (24.10.5 | --skip_cutadapt --skip_snpeff | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (latest-everything | --spades_mode metaviral | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (latest-everything | --spades_mode metaviral | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
Run pipeline with test data (24.10.5 | test | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Run pipeline with test data (24.10.5 | test | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
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)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
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)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (24.10.5 | --bowtie2_index ./GCA_009858895.3_ASM985889v3_genomic.200409.bt2.index.tar.gz | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (24.10.5 | --bowtie2_index ./GCA_009858895.3_ASM985889v3_genomic.200409.bt2.index.tar.gz | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
Test nanopore (24.10.5 | --artic_minion_caller medaka --sequencing_summary false --fast5_dir false --freyja_depthcutoff 1 | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Test nanopore (24.10.5 | --artic_minion_caller medaka --sequencing_summary false --fast5_dir false --freyja_depthcutoff 1 | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (24.10.5 | --spades_mode corona | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (24.10.5 | --spades_mode corona | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (24.10.5 | --consensus_caller ivar | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (24.10.5 | --consensus_caller ivar | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (24.10.5 | --skip_fastp --skip_pangolin | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (24.10.5 | --skip_fastp --skip_pangolin | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
Test nanopore (latest-everything | --artic_minion_caller medaka --sequencing_summary false --fast5_dir false --freyja_depthcutoff 1 | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Test nanopore (latest-everything | --artic_minion_caller medaka --sequencing_summary false --fast5_dir false --freyja_depthcutoff 1 | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (24.10.5 | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (24.10.5 | --additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (24.10.5 | --skip_plasmidid false | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (24.10.5 | --skip_plasmidid false | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (latest-everything | --skip_plasmidid false | docker)
The command [sudo apt-get remove -y '^mongodb-.*' --fix-missing] failed to complete successfully. Proceeding...
|
|
Test parameters (latest-everything | --skip_plasmidid false | docker)
The command [sudo apt-get remove -y azure-cli google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri --fix-missing] failed to complete successfully. Proceeding...
|