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 pipeline with Kallisto, skipping both QC and alignment
github-actions / JUnit Test Report
Test pipeline with Kallisto, skipping both QC and alignment.Params: --pseudo_aligner kallisto --skip_qc --skip_alignment
Assertion failed:
2 of 2 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.10.2
Launching `/home/runner/work/rnaseq/rnaseq/tests/../main.nf` [wise_leavitt] DSL2 - revision: 85c9b75b8b
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/./workflows/rnaseq/../../subworkflows/local/utils_nfcore_rnaseq_pipeline/../../nf-core/fastq_qc_trim_filter_setstrandedness/main.nf' at line: 7 or see '/home/runner/work/rnaseq/rnaseq/~/tests/3bdf2943960b42549e1eb2f05f2109d/meta/nextflow.log' file for more details
Nextflow stderr:
Check failure on line 1 in Test pipeline with Kallisto, skipping both QC and alignment
github-actions / JUnit Test Report
Test pipeline with Kallisto, skipping both QC and alignment.Params: --pseudo_aligner kallisto --skip_qc --skip_alignment - stub
Assertion failed:
2 of 2 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.10.2
Launching `/home/runner/work/rnaseq/rnaseq/tests/../main.nf` [modest_kare] DSL2 - revision: 85c9b75b8b
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/./workflows/rnaseq/../../subworkflows/local/utils_nfcore_rnaseq_pipeline/../../nf-core/fastq_qc_trim_filter_setstrandedness/main.nf' at line: 7 or see '/home/runner/work/rnaseq/rnaseq/~/tests/54655b7600b646af862a2f183d5309ad/meta/nextflow.log' file for more details
Nextflow stderr:
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