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Important! Template update for nf-core/tools v3.0.1 #3388

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Important! Template update for nf-core/tools v3.0.1

Important! Template update for nf-core/tools v3.0.1 #3388

Triggered via pull request October 9, 2024 17:23
@maxulyssemaxulysse
synchronize #1401
nf-core-template-merge-3.0.1
Status Success
Total duration 2m 21s
Artifacts 1

linting.yml

on: pull_request
pre-commit
16s
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nf-core
2m 11s
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8 errors and 1 warning
Test Subworkflow FASTQ_FASTQC_UMITOOLS_TRIMGALORE.test skip all steps: Test Subworkflow FASTQ_FASTQC_UMITOOLS_TRIMGALORE#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow FASTQ_FASTQC_UMITOOLS_TRIMGALORE.test skip all steps: Test Subworkflow FASTQ_FASTQC_UMITOOLS_TRIMGALORE#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with Kallisto, skipping both QC and alignment.Params: --pseudo_aligner kallisto --skip_qc --skip_alignment: Test pipeline with Kallisto, skipping both QC and alignment#L1
groovy.lang.MissingMethodException: No signature of method: kallisto_nf$_run_closure1$_closure2.getAllFilesFromDir() is applicable for argument types: (LinkedHashMap, org.codehaus.groovy.runtime.GStringImpl) values: [[relative:true, includeDir:true, ignore:[pipeline_info/*.{html,json,txt}]], /home/runner/work/rnaseq/rnaseq/~/tests/3bdf2943960b42549e1eb2f05f2109d/output]
Test pipeline with Salmon, skipping both QC and alignment.Params: --pseudo_aligner salmon --skip_qc --skip_alignment: Test pipeline with Salmon, skipping both QC and alignment#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with Salmon, skipping both QC and alignment.Params: --pseudo_aligner salmon --skip_qc --skip_alignment - stub: Test pipeline with Salmon, skipping both QC and alignment#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with Salmon, skipping both QC and alignment.Params: --pseudo_aligner salmon --skip_qc --skip_alignment: Test pipeline with Salmon, skipping both QC and alignment#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with Salmon, skipping both QC and alignment.Params: --pseudo_aligner salmon --skip_qc --skip_alignment - stub: Test pipeline with Salmon, skipping both QC and alignment#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with Kallisto, skipping both QC and alignment.Params: --pseudo_aligner kallisto --skip_qc --skip_alignment: Test pipeline with Kallisto, skipping both QC and alignment#L1
groovy.lang.MissingMethodException: No signature of method: kallisto_nf$_run_closure1$_closure2.getAllFilesFromDir() is applicable for argument types: (LinkedHashMap, org.codehaus.groovy.runtime.GStringImpl) values: [[relative:true, includeDir:true, ignore:[pipeline_info/*.{html,json,txt}]], /home/runner/work/rnaseq/rnaseq/~/tests/3bdf2943960b42549e1eb2f05f2109d/output]
nf-core
The following actions use a deprecated Node.js version and will be forced to run on node20: pietrobolcato/[email protected]. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/

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