New ivar_variants_to_vcf.py #173

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Re-run triggered May 17, 2024 07:59

svarona

#31

Shettland:dev

Status Cancelled

Total duration 25m 14s

Artifacts –

ci.yml

on: pull_request

Matrix: Test workflow parameters

Matrix: Run pipeline with test data

Matrix: Test Nanopore workflow

Matrix: Test SISPA workflow

Annotations

21 errors and 23 warnings

Run pipeline with test data (23.04.0)

The job was canceled because "latest-everything" failed.

Run pipeline with test data (23.04.0)

The operation was canceled.

Run pipeline with test data (latest-everything)

Process completed with exit code 1.

Test workflow parameters (--variant_caller bcftools --consensus_caller ivar)

The job was canceled because "_--skip_plasmidid_false_-" failed.

Test workflow parameters (--variant_caller bcftools --consensus_caller ivar)

The operation was canceled.

Test workflow parameters (--skip_variants)

The job was canceled because "_--skip_plasmidid_false_-" failed.

Test workflow parameters (--skip_variants)

The operation was canceled.

Test workflow parameters (--skip_fastp --skip_pangolin)

The job was canceled because "_--skip_plasmidid_false_-" failed.

Test workflow parameters (--skip_cutadapt --skip_snpeff)

The job was canceled because "_--skip_plasmidid_false_-" failed.

Test workflow parameters (--skip_cutadapt --skip_snpeff)

The operation was canceled.

Test workflow parameters (--skip_assembly)

The job was canceled because "_--skip_plasmidid_false_-" failed.

Test workflow parameters (--skip_assembly)

The operation was canceled.

Test workflow parameters (--skip_kraken2)

The job was canceled because "_--skip_plasmidid_false_-" failed.

Test workflow parameters (--skip_kraken2)

The operation was canceled.

Test workflow parameters (--spades_mode metaviral)

The job was canceled because "_--skip_plasmidid_false_-" failed.

Test workflow parameters (--spades_mode corona)

The job was canceled because "_--skip_plasmidid_false_-" failed.

Test workflow parameters (--spades_mode corona)

The operation was canceled.

Test workflow parameters (--skip_plasmidid false --skip_asciigenome)

Process completed with exit code 1.

Test workflow parameters (--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz)

The job was canceled because "_--skip_plasmidid_false_-" failed.

Test workflow parameters (--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz)

The operation was canceled.

Test workflow parameters (--consensus_caller ivar)

Process completed with exit code 1.

Test SISPA workflow (--genome 'NC_045512.2')

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 SISPA workflow (--genome 'NC_045512.2')

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 SISPA workflow (--gff false)

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 SISPA 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/

Run pipeline with test data (latest-everything)

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: nf-core/setup-nextflow@v1. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

Test Nanopore workflow (--gff false)

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 (--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 Nanopore workflow (--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz)

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 (--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz)

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)

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/

Test Nanopore workflow (--input false)

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 (--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 Nanopore workflow (--min_guppyplex_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_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 Nanopore workflow (--artic_minion_caller medaka --sequencing_summary false --fast5_dir false...

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 (--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)

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 (--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 workflow parameters (--skip_plasmidid false --skip_asciigenome)

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 workflow parameters (--skip_plasmidid false --skip_asciigenome)

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)

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 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/