nf-core CI

Important! Template update for nf-core/tools v3.0.2 #1032

Triggered via pull request October 14, 2024 10:22

maxulysse

synchronize #323

nf-core-template-merge-3.0.2

Status Failure

Total duration 12m 57s

Artifacts –

ci.yml

on: pull_request

Check for changes

16s

Matrix: test

confirm-pass

Annotations

35 errors and 59 warnings

Test Process UNTAR.test_untar: Test Process UNTAR#L1

Assertion failed: 2 of 2 assertions failed

Test Process UNTAR.test_untar_onlyfiles: Test Process UNTAR#L1

Assertion failed: 2 of 2 assertions failed

Test process: SRA_RUNINFO_TO_FTP.Should run without failures: Test process: SRA_RUNINFO_TO_FTP#L1

Assertion failed: 2 of 2 assertions failed

Test | modules/local/sra_runinfo_to_ftp/tests/main.nf.test | 24.04.2 | docker

Process completed with exit code 1.

Test | modules/nf-core/untar/tests/main.nf.test | latest-everything | docker

Process completed with exit code 1.

Test Process SRATOOLS_PREFETCH.sratools/prefetch: Test Process SRATOOLS_PREFETCH#L1

Assertion failed: 2 of 2 assertions failed

Test Process SRATOOLS_PREFETCH.sratools/prefetch with sralite: Test Process SRATOOLS_PREFETCH#L1

Assertion failed: 2 of 2 assertions failed

Test | modules/nf-core/sratools/prefetch/tests/main.nf.test | 24.04.2 | docker

Process completed with exit code 1.

Test Process UNTAR.test_untar: Test Process UNTAR#L1

Assertion failed: 2 of 2 assertions failed

Test Process UNTAR.test_untar_onlyfiles: Test Process UNTAR#L1

Assertion failed: 2 of 2 assertions failed

Test Process SRATOOLS_FASTERQDUMP.Single-end: Test Process SRATOOLS_FASTERQDUMP#L1

Assertion failed: 2 of 2 assertions failed

Test Process SRATOOLS_FASTERQDUMP.Paired-end: Test Process SRATOOLS_FASTERQDUMP#L1

Assertion failed: 2 of 2 assertions failed

Test Process CUSTOM_SRATOOLSNCBISETTINGS.Should run without failures: Test Process CUSTOM_SRATOOLSNCBISETTINGS#L1

Assertion failed: assert process.success | | | false CUSTOM_SRATOOLSNCBISETTINGS

Test | modules/nf-core/sratools/fasterqdump/tests/main.nf.test | 24.04.2 | docker

Process completed with exit code 1.

Test | modules/nf-core/untar/tests/main.nf.test | 24.04.2 | docker

Process completed with exit code 1.

Test | modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test | 24.04.2 | docker

Process completed with exit code 1.

Test process: MULTIQC_MAPPINGS_CONFIG.Should run without failures: Test process: MULTIQC_MAPPINGS_CONFIG#L1

Assertion failed: 2 of 2 assertions failed

Test Process SRATOOLS_FASTERQDUMP.Single-end: Test Process SRATOOLS_FASTERQDUMP#L1

Assertion failed: 2 of 2 assertions failed

Test Process SRATOOLS_FASTERQDUMP.Paired-end: Test Process SRATOOLS_FASTERQDUMP#L1

Assertion failed: 2 of 2 assertions failed

Test | modules/local/multiqc_mappings_config/tests/main.nf.test | 24.04.2 | docker

Process completed with exit code 1.

Test Process CUSTOM_SRATOOLSNCBISETTINGS.Should run without failures: Test Process CUSTOM_SRATOOLSNCBISETTINGS#L1

Assertion failed: assert process.success | | | false CUSTOM_SRATOOLSNCBISETTINGS

Test | modules/nf-core/sratools/fasterqdump/tests/main.nf.test | latest-everything | docker

Process completed with exit code 1.

Test | modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test | latest-everything | docker

Process completed with exit code 1.

Test Workflow PIPELINE_INITIALISATION.Should run: Test Workflow PIPELINE_INITIALISATION#L1

Assertion failed: 1 of 1 assertions failed

Test | subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test | 24.04.2 | docker

Process completed with exit code 1.

Test Workflow PIPELINE_INITIALISATION.Should run: Test Workflow PIPELINE_INITIALISATION#L1

Assertion failed: 1 of 1 assertions failed

Test | subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test | latest-everything | docker

Process completed with exit code 1.

Test Process SRATOOLS_PREFETCH.sratools/prefetch: Test Process SRATOOLS_PREFETCH#L1

Assertion failed: 2 of 2 assertions failed

Test Process SRATOOLS_PREFETCH.sratools/prefetch with sralite: Test Process SRATOOLS_PREFETCH#L1

Assertion failed: 2 of 2 assertions failed

Test | modules/nf-core/sratools/prefetch/tests/main.nf.test | latest-everything | docker

Process completed with exit code 1.

Test process: MULTIQC_MAPPINGS_CONFIG.Should run without failures: Test process: MULTIQC_MAPPINGS_CONFIG#L1

Assertion failed: 2 of 2 assertions failed

Test | modules/local/multiqc_mappings_config/tests/main.nf.test | latest-everything | docker

Process completed with exit code 1.

Test process: SRA_RUNINFO_TO_FTP.Should run without failures: Test process: SRA_RUNINFO_TO_FTP#L1

Assertion failed: 2 of 2 assertions failed

Test | modules/local/sra_runinfo_to_ftp/tests/main.nf.test | latest-everything | docker

Process completed with exit code 1.

confirm-pass

Process completed with exit code 1.

Check for changes

The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/

Test | modules/local/sra_runinfo_to_ftp/tests/main.nf.test | 24.04.2 | docker

The following actions use a deprecated Node.js version and will be forced to run on node20: actions/setup-python@v4, mikepenz/action-junit-report@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/

Test | modules/nf-core/untar/tests/main.nf.test | latest-everything | docker

Test | modules/local/sra_to_samplesheet/tests/main.nf.test | 24.04.2 | docker

Test | subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test | 24.04.2 | docker

Test | modules/nf-core/sratools/prefetch/tests/main.nf.test | 24.04.2 | docker

Test | workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test | 24.04.2 | docker

Test | subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.nf.test | 24.04.2 | docker

Test | subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test | latest-everything | docker

Test | workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test | 24.04.2 | docker

Test | modules/nf-core/sratools/fasterqdump/tests/main.nf.test | 24.04.2 | docker

Test | modules/nf-core/untar/tests/main.nf.test | 24.04.2 | docker

Test | subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test | 24.04.2 | docker

Test | modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test | 24.04.2 | docker

Test | modules/local/sra_fastq_ftp/tests/main.nf.test | 24.04.2 | docker

Test | workflows/sra/tests/sra_skip_fastq_download.nf.test | latest-everything | docker

Test | workflows/sra/tests/sra_skip_fastq_download.nf.test | 24.04.2 | docker

Test | modules/local/multiqc_mappings_config/tests/main.nf.test | 24.04.2 | docker

Test | workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test | 24.04.2 | docker

Test | modules/nf-core/sratools/fasterqdump/tests/main.nf.test | latest-everything | docker

Test | modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test | latest-everything | docker

Test | workflows/sra/tests/sra_download_method_aspera.nf.test | latest-everything | docker

Test | subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test | 24.04.2 | docker

Test | subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test | latest-everything | docker

Test | subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test | latest-everything | docker

Test | subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.function.nf.test | latest-everything | docker

Test | subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test | 24.04.2 | docker

Test | workflows/sra/tests/sra_download_method_sratools.nf.test | 24.04.2 | docker

Test | modules/local/aspera_cli/tests/main.nf.test | 24.04.2 | docker

Test | subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test | 24.04.2 | docker

Test | modules/local/sra_ids_to_runinfo/tests/main.nf.test | 24.04.2 | docker

Test | workflows/sra/tests/main.nf.test | 24.04.2 | docker

Test | subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test | 24.04.2 | docker

Test | workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test | latest-everything | docker

Test | workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test | 24.04.2 | docker

Test | subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test | latest-everything | docker

Test | modules/local/sra_ids_to_runinfo/tests/main.nf.test | latest-everything | docker

Test | workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test | latest-everything | docker

Test | workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test | 24.04.2 | docker

Test | subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test | 24.04.2 | docker

Test | workflows/sra/tests/sra_download_method_aspera.nf.test | 24.04.2 | docker

Test | subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test | 24.04.2 | docker

Test | subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test | latest-everything | docker

Test | workflows/sra/tests/sra_download_method_sratools.nf.test | latest-everything | docker

Test | subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.nf.test | latest-everything | docker

Test | subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test | latest-everything | docker

Test | tests/main.nf.test | latest-everything | docker

Test | modules/local/sra_fastq_ftp/tests/main.nf.test | latest-everything | docker

Test | modules/nf-core/sratools/prefetch/tests/main.nf.test | latest-everything | docker

Test | tests/main.nf.test | 24.04.2 | docker

Test | modules/local/aspera_cli/tests/main.nf.test | latest-everything | docker

Test | modules/local/multiqc_mappings_config/tests/main.nf.test | latest-everything | docker

Test | modules/local/sra_to_samplesheet/tests/main.nf.test | latest-everything | docker

Test | workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test | latest-everything | docker

Test | workflows/sra/tests/main.nf.test | latest-everything | docker

Test | workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test | latest-everything | docker

Test | modules/local/sra_runinfo_to_ftp/tests/main.nf.test | latest-everything | docker

Test | workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test | latest-everything | docker

Test | subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test | latest-everything | docker

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Important! Template update for nf-core/tools v3.0.2 #1032

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