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New ivar_variants_to_vcf.py #175

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New ivar_variants_to_vcf.py

New ivar_variants_to_vcf.py #175

Triggered via pull request May 21, 2024 12:24
@ShettlandShettland
opened #32
Shettland:develop
Status Cancelled
Total duration 1h 19m 56s
Artifacts –

ci.yml

on: pull_request
Matrix: Test workflow parameters
Matrix: Run pipeline with test data
Matrix: Test Nanopore workflow
Matrix: Test SISPA workflow
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76 errors and 2 warnings
Test Nanopore workflow (--artic_minion_caller medaka --sequencing_summary false --fast5_dir false...
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test Nanopore workflow (--artic_minion_caller medaka --sequencing_summary false --fast5_dir false...
The operation was canceled.
Test workflow parameters (--skip_variants)
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test workflow parameters (--skip_variants)
The operation was canceled.
Test Nanopore workflow (--gff false)
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test Nanopore workflow (--gff false)
The operation was canceled.
Test workflow parameters (--skip_plasmidid false --skip_asciigenome)
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test workflow parameters (--variant_caller bcftools --consensus_caller ivar)
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test workflow parameters (--variant_caller bcftools --consensus_caller ivar)
The operation was canceled.
Test workflow parameters (--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz)
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test workflow parameters (--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz)
The operation was canceled.
Test Nanopore workflow (--artic_minion_caller medaka --sequencing_summary false --fast5_dir false)
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test Nanopore workflow (--artic_minion_caller medaka --sequencing_summary false --fast5_dir false)
The operation was canceled.
Test workflow parameters (--skip_fastp --skip_pangolin)
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test workflow parameters (--skip_cutadapt --skip_snpeff)
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test workflow parameters (--skip_fastp --skip_pangolin)
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test workflow parameters (--skip_fastp --skip_pangolin)
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test workflow parameters (--skip_fastp --skip_pangolin)
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Run pipeline with test data (23.04.0)
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test workflow parameters (--spades_mode metaviral)
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test workflow parameters (--spades_mode metaviral)
The operation was canceled.
Test SISPA workflow (--gff false)
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test Nanopore workflow (--input false)
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test Nanopore workflow (--input false)
The operation was canceled.
Run pipeline with test data (latest-everything)
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Run pipeline with test data (latest-everything)
The operation was canceled.
Test workflow parameters (--skip_kraken2)
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test workflow parameters (--skip_kraken2)
The operation was canceled.
Test Nanopore workflow (--input false)
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test Nanopore workflow (--input false)
The operation was canceled.
Test Nanopore workflow (--input false)
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test Nanopore workflow (--input false)
The operation was canceled.
Test Nanopore workflow (--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz)
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test Nanopore workflow (--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz)
The operation was canceled.
Test SISPA workflow (--genome 'NC_045512.2')
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test SISPA workflow (--genome 'NC_045512.2')
The operation was canceled.
Test workflow parameters (--consensus_caller ivar)
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test workflow parameters (--consensus_caller ivar)
The operation was canceled.
Test Nanopore workflow (--input false)
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test Nanopore workflow (--input false)
The operation was canceled.
Test workflow parameters (--spades_mode corona)
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test SISPA workflow (--genome 'NC_045512.2')
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test SISPA workflow (--genome 'NC_045512.2')
The operation was canceled.
Test workflow parameters (--spades_mode corona)
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test SISPA workflow (--genome 'NC_045512.2')
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test SISPA workflow (--genome 'NC_045512.2')
The operation was canceled.
Test workflow parameters (--spades_mode corona)
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test SISPA workflow (--genome 'NC_045512.2')
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test SISPA workflow (--genome 'NC_045512.2')
The operation was canceled.
Test workflow parameters (--spades_mode corona)
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test workflow parameters (--skip_assembly)
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test Nanopore workflow (--min_guppyplex_reads 10000)
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test Nanopore workflow (--min_guppyplex_reads 10000)
The operation was canceled.
Test workflow parameters (--skip_fastp --skip_pangolin)
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test Nanopore workflow (--input false)
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test Nanopore workflow (--input false)
The operation was canceled.
Test Nanopore workflow (--input false)
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test Nanopore workflow (--input false)
The operation was canceled.
Test SISPA workflow (--genome 'NC_045512.2')
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test SISPA workflow (--genome 'NC_045512.2')
The operation was canceled.
Test Nanopore workflow (--input false)
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test Nanopore workflow (--input false)
The operation was canceled.
Test Nanopore workflow (--input false)
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test Nanopore workflow (--input false)
The operation was canceled.
Test workflow parameters (--spades_mode corona)
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test workflow parameters (--spades_mode corona)
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test Nanopore workflow (--input false)
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test Nanopore workflow (--input false)
The operation was canceled.
Test Nanopore workflow (--input false)
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test Nanopore workflow (--input false)
The operation was canceled.
Test Nanopore workflow (--input false)
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test Nanopore workflow (--input false)
The operation was canceled.
Test Nanopore workflow (--input false)
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test Nanopore workflow (--input false)
The operation was canceled.
Test Nanopore workflow (--input false)
Canceling since a higher priority waiting request for 'nf-core CI-32' exists
Test Nanopore workflow (--input false)
The operation was canceled.
Test Nanopore workflow (--min_barcode_reads 10000)
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v2. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
Test Nanopore workflow (--min_barcode_reads 10000)
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/