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Changed Cutadapt to use nf-core modules #1342

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Changed Cutadapt to use nf-core modules

Changed Cutadapt to use nf-core modules #1342

Re-run triggered October 7, 2024 18:19
@maxulyssemaxulysse
#435
BU-ISCIII:cutadapt
Status Failure
Total duration 6m 13s
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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Annotations

18 errors and 26 warnings
Test workflow parameters (--skip_variants)
Process completed with exit code 1.
Test workflow parameters (--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz)
The job was canceled because "_--skip_variants" failed.
Test workflow parameters (--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz)
The operation was canceled.
Test workflow parameters (--skip_kraken2)
The job was canceled because "_--skip_variants" failed.
Test workflow parameters (--skip_kraken2)
The operation was canceled.
Test workflow parameters (--spades_mode corona)
The job was canceled because "_--skip_variants" failed.
Test workflow parameters (--spades_mode corona)
The operation was canceled.
Test workflow parameters (--skip_assembly)
The job was canceled because "_--skip_variants" failed.
Test workflow parameters (--skip_assembly)
The operation was canceled.
Test workflow parameters (--skip_cutadapt --skip_snpeff)
The job was canceled because "_--skip_variants" failed.
Test workflow parameters (--skip_cutadapt --skip_snpeff)
The operation was canceled.
Test workflow parameters (--spades_mode metaviral)
The job was canceled because "_--skip_variants" failed.
Test workflow parameters (--spades_mode metaviral)
The operation was canceled.
Test workflow parameters (--skip_fastp --skip_pangolin)
The job was canceled because "_--skip_variants" failed.
Test workflow parameters (--skip_fastp --skip_pangolin)
The operation was canceled.
Test workflow parameters (--skip_plasmidid false --skip_asciigenome)
The job was canceled because "_--skip_variants" failed.
Test workflow parameters (--skip_plasmidid false --skip_asciigenome)
The operation was canceled.
Run pipeline with test data (23.04.0)
Process completed with exit code 1.
Test workflow parameters (--bowtie2_index ./GCA_009858895.3_ASM985889v3_genomic.200409.bt2.index....
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 (--bowtie2_index ./GCA_009858895.3_ASM985889v3_genomic.200409.bt2.index....
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 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 (--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 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 --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 (--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 (--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 (--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 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 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 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 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 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 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/