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Adding new nf-core subworkflow freyja for weighted variant analysis #1237

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Adding new nf-core subworkflow freyja for weighted variant analysis

Adding new nf-core subworkflow freyja for weighted variant analysis #1237

Triggered via pull request August 16, 2023 08:31
@Joon-KlapsJoon-Klaps
synchronize #375
Joon-Klaps:freyja
Status Cancelled
Total duration 19m 12s
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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22 errors and 9 warnings
Test workflow parameters (--skip_fastp --skip_pangolin)
Canceling since a higher priority waiting request for 'nf-core CI-375' exists
Test workflow parameters (--skip_variants)
Canceling since a higher priority waiting request for 'nf-core CI-375' exists
Test workflow parameters (--skip_plasmidid false --skip_asciigenome)
Canceling since a higher priority waiting request for 'nf-core CI-375' exists
Test workflow parameters (--skip_kraken2)
Canceling since a higher priority waiting request for 'nf-core CI-375' exists
Test SISPA workflow (--genome 'NC_045512.2')
Canceling since a higher priority waiting request for 'nf-core CI-375' exists
Test workflow parameters (--variant_caller bcftools --consensus_caller ivar)
Canceling since a higher priority waiting request for 'nf-core CI-375' exists
Test SISPA workflow (--gff false)
Canceling since a higher priority waiting request for 'nf-core CI-375' exists
Test workflow parameters (--spades_mode corona)
Canceling since a higher priority waiting request for 'nf-core CI-375' exists
Test workflow parameters (--spades_mode metaviral)
Canceling since a higher priority waiting request for 'nf-core CI-375' exists
Test Nanopore workflow (--gff false)
The operation was canceled.
Test workflow parameters (--skip_assembly)
The operation was canceled.
Run pipeline with test data (latest-everything)
Canceling since a higher priority waiting request for 'nf-core CI-375' exists
Run pipeline with test data (latest-everything)
The operation was canceled.
Test Nanopore workflow (--artic_minion_caller medaka --sequencing_summary false --fast5_dir false...
The operation was canceled.
Test Nanopore workflow (--artic_minion_caller medaka --sequencing_summary false --fast5_dir false)
The operation was canceled.
Test Nanopore workflow (--min_guppyplex_reads 10000)
The operation was canceled.
Test workflow parameters (--consensus_caller ivar)
The operation was canceled.
Test Nanopore workflow (--min_barcode_reads 10000)
The operation was canceled.
Run pipeline with test data (22.10.1)
Canceling since a higher priority waiting request for 'nf-core CI-375' exists
Run pipeline with test data (22.10.1)
The operation was canceled.
Test Nanopore workflow (--input false)
The operation was canceled.
Test workflow parameters (--skip_cutadapt --skip_snpeff)
The operation was canceled.
Test Nanopore workflow (--gff false)
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/
Test workflow parameters (--skip_assembly)
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/
Test Nanopore workflow (--artic_minion_caller medaka --sequencing_summary false --fast5_dir false...
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/
Test Nanopore workflow (--artic_minion_caller medaka --sequencing_summary false --fast5_dir false)
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/
Test Nanopore workflow (--min_guppyplex_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/
Test workflow parameters (--consensus_caller ivar)
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/
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/
Test Nanopore workflow (--input false)
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/
Test workflow parameters (--skip_cutadapt --skip_snpeff)
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/