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Merge pull request #438 from nf-core/update-fastp #1334

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Merge pull request #438 from nf-core/update-fastp

Merge pull request #438 from nf-core/update-fastp #1334

Triggered via push July 31, 2024 08:20
@Joon-KlapsJoon-Klaps
pushed 50992ea
dev
Status Success
Total duration 31m 30s
Artifacts –

ci.yml

on: push
Matrix: Test workflow parameters
Matrix: Run pipeline with test data
Matrix: Test Nanopore workflow
Matrix: Test SISPA workflow
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40 warnings
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 (--min_barcode_reads 10000)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v2. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-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 Nanopore workflow (--min_guppyplex_reads 10000)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v2. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
Test workflow parameters (--skip_variants)
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_variants)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v2. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
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/
Test SISPA workflow (--gff false)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v2. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
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 (--genome 'NC_045512.2')
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v2. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
Test Nanopore workflow (--gff false --freyja_depthcutoff 1)
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 (--gff false --freyja_depthcutoff 1)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v2. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-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/
Test workflow parameters (--skip_cutadapt --skip_snpeff)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v2. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-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 workflow parameters (--skip_assembly)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v2. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
Test workflow parameters (--variant_caller bcftools --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 workflow parameters (--variant_caller bcftools --consensus_caller ivar)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v2. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-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 workflow parameters (--consensus_caller ivar)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v2. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
Test workflow parameters (--spades_mode corona)
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 (--spades_mode corona)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v2. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
Test Nanopore workflow (--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz --fr...
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 --fr...
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v2. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
Test workflow parameters (--skip_fastp --skip_pangolin)
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_fastp --skip_pangolin)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v2. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
Test workflow parameters (--spades_mode metaviral)
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 (--spades_mode metaviral)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v2. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
Test workflow parameters (--skip_kraken2)
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_kraken2)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v2. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
Test workflow parameters (--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 workflow parameters (--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v2. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
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 (--skip_plasmidid false --skip_asciigenome)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v2. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
Test Nanopore workflow (--input false --freyja_depthcutoff 1)
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 --freyja_depthcutoff 1)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v2. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-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 use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v2. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-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 use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v2. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/