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DSL2+ #1250

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DSL2+

DSL2+ #1250

Triggered via pull request December 5, 2024 00:14
@bentshermanbentsherman
synchronize #312
dsl2-plus
Status Failure
Total duration 1m 15s
Artifacts 1

linting.yml

on: pull_request
pre-commit
24s
pre-commit
nf-core
1m 5s
nf-core
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49 errors and 2 warnings
nf-core
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 Workflow UTILS_NFCORE_PIPELINE.Should run without failures: Test Workflow UTILS_NFCORE_PIPELINE#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
nf.Parameters: --nf_core_pipeline viralrecon: nf#L1
Assertion failed: 2 of 2 assertions failed
nf.Parameters: --nf_core_pipeline taxprofiler: nf#L1
Assertion failed: 2 of 2 assertions failed
nf.Parameters: --skip_fastq_download: nf#L1
Assertion failed: 2 of 2 assertions failed
Test Functions.Function isSraId: Test Functions#L1
Assertion failed: 2 of 2 assertions failed
Test Functions.Function sraCheckENAMetadataFields [success]: Test Functions#L1
Assertion failed: 1 of 2 assertions failed
Test Functions.Function sraCurateSamplesheetWarn: Test Functions#L1
Assertion failed: 1 of 2 assertions failed
nf.Parameters: --download_method sratools: nf#L1
Assertion failed: 2 of 2 assertions failed
nf.Parameters: --nf_core_pipeline rnaseq: nf#L1
Assertion failed: 2 of 2 assertions failed
nf.Parameters: default: nf#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 Workflow PIPELINE_INITIALISATION.Should run: Test Workflow PIPELINE_INITIALISATION#L1
Assertion failed: 1 of 1 assertions failed
Test process: SRA_FASTQ_FTP.Should run without failures: Test process: SRA_FASTQ_FTP#L1
Assertion failed: 2 of 2 assertions failed
nf.Parameters: --nf_core_pipeline atacseq: nf#L1
Assertion failed: 2 of 2 assertions failed
Test process: SRA_IDS_TO_RUNINFO.Should run without failures: Test process: SRA_IDS_TO_RUNINFO#L1
Assertion failed: 2 of 2 assertions failed
Test process: MULTIQC_MAPPINGS_CONFIG.Should run without failures: Test process: MULTIQC_MAPPINGS_CONFIG#L1
Assertion failed: 2 of 2 assertions failed
Test Workflow PIPELINE_COMPLETION.Should run: Test Workflow PIPELINE_COMPLETION#L1
Assertion failed: 1 of 1 assertions failed
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
nf.Parameters: --nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...: nf#L1
Assertion failed: 2 of 2 assertions failed
Test Functions.Test Function checkConfigProvided: Test Functions#L1
Assertion failed: 2 of 2 assertions failed
Test Functions.Test Function checkProfileProvided: Test Functions#L1
Assertion failed: 1 of 2 assertions failed
Test Functions.Test Function workflowCitation: Test Functions#L1
Assertion failed: 2 of 2 assertions failed
Test Functions.Test Function nfCoreLogo: Test Functions#L1
Assertion failed: 2 of 2 assertions failed
Test Functions.Test Function dashedLine: Test Functions#L1
Assertion failed: 2 of 2 assertions failed
Test Functions.Test Function without logColours: Test Functions#L1
Assertion failed: 2 of 2 assertions failed
Test Functions.Test Function with logColours: Test Functions#L1
Assertion failed: 2 of 2 assertions failed
nf.Parameters: --download_method aspera: nf#L1
Assertion failed: 2 of 2 assertions failed
Test process: SRA_TO_SAMPLESHEET.Should run without failures: Test process: SRA_TO_SAMPLESHEET#L1
Assertion failed: 2 of 2 assertions failed
nf.Parameters: default: nf#L1
java.lang.RuntimeException: Workflow has no output channels. workflow.out can not be used.
Test Workflow UTILS_NEXTFLOW_PIPELINE.Should run no inputs: Test Workflow UTILS_NEXTFLOW_PIPELINE#L1
Assertion failed: 1 of 1 assertions failed
Test Workflow UTILS_NEXTFLOW_PIPELINE.Should print version: Test Workflow UTILS_NEXTFLOW_PIPELINE#L1
Assertion failed: 2 of 2 assertions failed
Test Workflow UTILS_NEXTFLOW_PIPELINE.Should dump params: Test Workflow UTILS_NEXTFLOW_PIPELINE#L1
Assertion failed: 1 of 1 assertions failed
Test Workflow UTILS_NEXTFLOW_PIPELINE.Should not create params JSON if no output directory: Test Workflow UTILS_NEXTFLOW_PIPELINE#L1
Assertion failed: 1 of 1 assertions failed
Test Subworkflow UTILS_NFSCHEMA_PLUGIN.Should run nothing: Test Subworkflow UTILS_NFSCHEMA_PLUGIN#L1
Assertion failed: 1 of 1 assertions failed
Test Subworkflow UTILS_NFSCHEMA_PLUGIN.Should validate params: Test Subworkflow UTILS_NFSCHEMA_PLUGIN#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow UTILS_NFSCHEMA_PLUGIN.Should run nothing - custom schema: Test Subworkflow UTILS_NFSCHEMA_PLUGIN#L1
Assertion failed: 1 of 1 assertions failed
Test Subworkflow UTILS_NFSCHEMA_PLUGIN.Should validate params - custom schema: Test Subworkflow UTILS_NFSCHEMA_PLUGIN#L1
Assertion failed: 1 of 2 assertions failed
Test Functions.Test Function getWorkflowVersion: Test Functions#L1
Assertion failed: 2 of 2 assertions failed
Test Functions.Test Function dumpParametersToJSON: Test Functions#L1
Assertion failed: 1 of 1 assertions failed
Test Functions.Test Function checkCondaChannels: Test Functions#L1
Assertion failed: 1 of 2 assertions failed
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 Process SRATOOLS_PREFETCH.sratools/prefetch/stub: Test Process SRATOOLS_PREFETCH#L1
Assertion failed: 2 of 2 assertions failed
Test process: ASPERA_CLI.Should run without failures: Test process: ASPERA_CLI#L1
Assertion failed: 2 of 2 assertions failed
pre-commit
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
nf-core
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

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