Add FASTQ linting during preprocessing #136
GitHub Actions / JUnit Test Report
failed
Dec 2, 2024 in 0s
2 tests run, 0 passed, 0 skipped, 2 failed.
Annotations
Check failure on line 1 in Test Subworkflow FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS
github-actions / JUnit Test Report
Test Subworkflow FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS.homo_sapiens paired-end [fastq] fastp
java.lang.RuntimeException: Workflow has no output channels. workflow.out can not be used.
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.10.2
Launching `/home/runner/work/rnaseq/rnaseq/.nf-test-b6b0d6658ea42f84a1b8cf824576357.nf` [lethal_ekeblad] DSL2 - revision: 7ba90e0024
Downloading plugin [email protected]
ERROR ~ No such file or directory: Can't find a matching module file for include: ../../../modules/nf-core/fq/lint/main
-- Check script '/home/runner/work/rnaseq/rnaseq/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/tests/../main.nf' at line: 7 or see '/home/runner/work/rnaseq/rnaseq/~/tests/b6b0d6658ea42f84a1b8cf824576357/meta/nextflow.log' file for more details
Nextflow stderr:
Check failure on line 1 in Test Subworkflow FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS
github-actions / JUnit Test Report
Test Subworkflow FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS.homo_sapiens paired-end [fastq] trimgalore
java.lang.RuntimeException: Workflow has no output channels. workflow.out can not be used.
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.10.2
Launching `/home/runner/work/rnaseq/rnaseq/.nf-test-2aad29fde9a6d172dcb1afff2e9f9bc3.nf` [stupefied_becquerel] DSL2 - revision: 7ba90e0024
ERROR ~ No such file or directory: Can't find a matching module file for include: ../../../modules/nf-core/fq/lint/main
-- Check script '/home/runner/work/rnaseq/rnaseq/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/tests/../main.nf' at line: 7 or see '/home/runner/work/rnaseq/rnaseq/~/tests/2aad29fde9a6d172dcb1afff2e9f9bc3/meta/nextflow.log' file for more details
Nextflow stderr:
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