8000 Fix full test gha (#1802) · nf-core/sarek@984d871 · GitHub
[go: up one dir, main page]
More Web Proxy on the site http://driver.im/
Skip to content
nf-core CI

Fix full test gha (#1802) #6733

Sign in to view logs

Fix full test gha (#1802)

Fix full test gha (#1802) #6733

Triggered via push February 17, 2025 15:03
@maxulyssemaxulysse
pushed 984d871
dev
Status Success
Total duration 11m 19s
Artifacts –

ci.yml

on: push
Matrix: test
Fit to window
Zoom out
Zoom in

Annotations

59 errors and 30 warnings
Test pipeline.Run with profile test | --tools merge: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test sentieon.stub: Test sentieon#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline when starting from prepare recalibration.Run with profile test | --input tests/csv/3.0/mapped_single_bam.csv --step prepare_recalibration --tools null : Test pipeline when starting from prepare recalibration#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline.Run with profile test | --tools controlfreec --no_intervals | tumoronly: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline when starting from markduplicates.Run with profile test | --input tests/csv/3.0/mapped_single_cram.csv --step markduplicates --skip_tools markduplicates --tools null : Test pipeline when starting from markduplicates#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline.Run with profile test | --tools merge,snpeff,vep: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline.Run with profile test | --tools controlfreec --no_intervals | somatic | stub: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline.Run with profile test | --tools strelka | somatic: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline.Run with profile test | --tools strelka --no_intervals | somatic: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline.Run with profile test: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline.Run with profile test | --input tests/csv/3.0/fastq_pair.csv: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline.Run with profile test | --tools strelka --only_paired_variant_calling: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline.Run with profile test | --tools manta,strelka | somatic: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline.Run with profile test | --tools vep --download_cache --vep_include_fasta: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline when starting from markduplicates.Run with profile test | --input tests/csv/3.0/mapped_single_cram.csv --step markduplicates --skip_tools markduplicates --tools null : Test pipeline when starting from markduplicates#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline.Run with profile test | --tools controlfreec | somatic: Test pipeline#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline.Run with profile test | --tools manta,strelka --no_intervals | somatic: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline.Run with profile test | --aligner bwa-mem2 --save_reference | skip QC/recal/md: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline.Run with profile test | --tools strelka --no_intervals | somatic: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline.Run with profile test | --tools merge: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline.Run with profile test | --tools controlfreec --no_intervals | tumoronly: Test pipeline#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline.Run with profile test | --input tests/csv/3.0/fastq_pair.csv: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline.Run with profile test | --tools strelka --only_paired_variant_calling: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline.Run with profile test | --tools manta,strelka | somatic: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline.Run with profile test | --tools vep --download_cache --vep_include_fasta: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline.Run with profile test | --tools controlfreec | somatic: Test pipeline#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline.Run with profile test | --tools manta,strelka --no_intervals | somatic: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline.Run with profile test | --tools merge,snpeff,vep: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline.Run with profile test | --tools strelka | somatic: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline.Run with profile test | --tools vep --download_cache --vep_include_fasta: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline when starting from markduplicates.Run with profile test | --input tests/csv/3.0/mapped_single_cram.csv --step markduplicates --skip_tools markduplicates --tools null : Test pipeline when starting from markduplicates#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline when starting from recalibration.Run with profile test | --input tests/csv/3.0/mapped_single_bam.csv --step recalibrate --tools null : Test pipeline when starting from recalibration#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline.Run with profile test | --tools controlfreec | somatic: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline.Run with profile test | --tools manta,strelka --no_intervals | somatic: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline when starting from markduplicates.Run with profile test | --input tests/csv/3.0/mapped_single_bam.csv --step markduplicates --skip_tools markduplicates --tools null : Test pipeline when starting from markduplicates#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline when starting from prepare recalibration.Run with profile test | --input tests/csv/3.0/mapped_single_cram.csv --step prepare_recalibration --tools null : Test pipeline when starting from prepare recalibration#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline.Run with profile test | --tools controlfreec | tumoronly | stub: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline.Run with profile test | --tools strelka --no_intervals | somatic: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline.Run with profile test | --tools merge,snpeff,vep: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline when starting from recalibration.Run with profile test | --input tests/csv/3.0/mapped_single_cram.csv --step recalibrate --tools null : Test pipeline when starting from recalibration#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline.Run with profile test | --tools controlfreec --no_intervals | somatic | stub: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline.Run with profile test | --tools strelka | somatic: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline.Run with profile test | --tools merge: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test sentieon.stub: Test sentieon#L1
Assertion failed: 2 of 2 assertions failed
F438 Test pipeline.Run with profile test | --tools controlfreec --no_intervals | tumoronly: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline.Run with profile test | --input tests/csv/3.0/fastq_pair.csv: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline.Run with profile test | --tools strelka --only_paired_variant_calling: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline.Run with profile test | --tools manta,strelka | somatic: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline.Run with profile test | --tools merge: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline.Run with profile test | --tools controlfreec --no_intervals | tumoronly: Test pipeline#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline.Run with profile test | --tools strelka --no_intervals | somatic: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline.Run with profile test | --tools merge,snpeff,vep: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline.Run with profile test | --tools strelka | somatic: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline.Run with profile test | --tools vep --download_cache --vep_include_fasta: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline.Run with profile test | --tools controlfreec | somatic: Test pipeline#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline.Run with profile test | --tools manta,strelka --no_intervals | somatic: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline.Run with profile test | --input tests/csv/3.0/fastq_pair.csv: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline.Run with profile test | --tools strelka --only_paired_variant_calling: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline.Run with profile test | --tools manta,strelka | somatic: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test function | docker | 24.04.2 | 2/5
Your workflow is using a version of actions/cache that is scheduled for deprecation, actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9. Please update your workflow to use either v3 or v4 of actions/cache to avoid interruptions. Learn more: https://github.blog/changelog/2024-12-05-notice-of-upcoming-releases-and-breaking-changes-for-github-actions/#actions-cache-v1-v2-and-actions-toolkit-cache-package-closing-down
Test function | docker | 24.04.2 | 3/5
Your workflow is using a version of actions/cache that is scheduled for deprecation, actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9. Please update your workflow to use either v3 or v4 of actions/cache to avoid interruptions. Learn more: https://github.blog/changelog/2024-12-05-notice-of-upcoming-releases-and-breaking-changes-for-github-actions/#actions-cache-v1-v2-and-actions-toolkit-cache-package-closing-down
Test function | docker | 24.04.2 | 4/5
Your workflow is using a version of actions/cache that is scheduled for deprecation, actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9. Please update your workflow to use either v3 or v4 of actions/cache to avoid interruptions. Learn more: https://github.blog/changelog/2024-12-05-notice-of-upcoming-releases-and-breaking-changes-for-github-actions/#actions-cache-v1-v2-and-actions-toolkit-cache-package-closing-down
Test function | docker | 24.04.2 | 5/5
Your workflow is using a version of actions/cache that is scheduled for deprecation, actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9. Please update your workflow to use either v3 or v4 of actions/cache to avoid interruptions. Learn more: https://github.blog/changelog/2024-12-05-notice-of-upcoming-releases-and-breaking-changes-for-github-actions/#actions-cache-v1-v2-and-actions-toolkit-cache-package-closing-down
Test function | docker | 24.04.2 | 1/5
Your workflow is using a version of actions/cache that is scheduled for deprecation, actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9. Please update your workflow to use either v3 or v4 of actions/cache to avoid interruptions. Learn more: https://github.blog/changelog/2024-12-05-notice-of-upcoming-releases-and-breaking-changes-for-github-actions/#actions-cache-v1-v2-and-actions-toolkit-cache-package-closing-down
Test pipeline | docker | 24.04.2 | 2/5
Your workflow is using a version of actions/cache that is scheduled for deprecation, actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9. Please update your workflow to use either v3 or v4 of actions/cache to avoid interruptions. Learn more: https://github.blog/changelog/2024-12-05-notice-of-upcoming-releases-and-breaking-changes-for-github-actions/#actions-cache-v1-v2-and-actions-toolkit-cache-package-closing-down
Test pipeline | docker | 24.04.2 | 3/5
Your workflow is using a version of actions/cache that is scheduled for deprecation, actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9. Please update your workflow to use either v3 or v4 of actions/cache to avoid interruptions. Learn more: https://github.blog/changelog/2024-12-05-notice-of-upcoming-releases-and-breaking-changes-for-github-actions/#actions-cache-v1-v2-and-actions-toolkit-cache-package-closing-down
Test pipeline | docker | 24.04.2 | 5/5
Your workflow is using a version of actions/cache that is scheduled for deprecation, actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9. Please update your workflow to use either v3 or v4 of actions/cache to avoid interruptions. Learn more: https://github.blog/changelog/2024-12-05-notice-of-upcoming-releases-and-breaking-changes-for-github-actions/#actions-cache-v1-v2-and-actions-toolkit-cache-package-closing-down
Test pipeline | docker | 24.04.2 | 4/5
Your workflow is using a version of actions/cache that is scheduled for deprecation, actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9. Please update your workflow to use either v3 or v4 of actions/cache to avoid interruptions. Learn more: https://github.blog/changelog/2024-12-05-notice-of-upcoming-releases-and-breaking-changes-for-github-actions/#actions-cache-v1-v2-and-actions-toolkit-cache-package-closing-down
Test workflow | docker | 24.04.2 | 2/5
Your workflow is using a version of actions/cache that is scheduled for deprecation, actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9. Please update your workflow to use either v3 or v4 of actions/cache to avoid interruptions. Learn more: https://github.blog/changelog/2024-12-05-notice-of-upcoming-releases-and-breaking-changes-for-github-actions/#actions-cache-v1-v2-and-actions-toolkit-cache-package-closing-down
Test pipeline | docker | 24.04.2 | 1/5
Your workflow is using a version of actions/cache that is scheduled for deprecation, actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9. Please update your workflow to use either v3 or v4 of actions/cache to avoid interruptions. Learn more: https://github.blog/changelog/2024-12-05-notice-of-upcoming-releases-and-breaking-changes-for-github-actions/#actions-cache-v1-v2-and-actions-toolkit-cache-package-closing-down
Test workflow | docker | 24.04.2 | 3/5
Your workflow is using a version of actions/cache that is scheduled for deprecation, actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9. Please update your workflow to use either v3 or v4 of actions/cache to avoid interruptions. Learn more: https://github.blog/changelog/2024-12-05-notice-of-upcoming-releases-and-breaking-changes-for-github-actions/#actions-cache-v1-v2-and-actions-toolkit-cache-package-closing-down
Test workflow | docker | 24.04.2 | 4/5
Your workflow is using a version of actions/cache that is scheduled for deprecation, actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9. Please update your workflow to use either v3 or v4 of actions/cache to avoid interruptions. Learn more: https://github.blog/changelog/2024-12-05-notice-of-upcoming-releases-and-breaking-changes-for-github-actions/#actions-cache-v1-v2-and-actions-toolkit-cache-package-closing-down
Test workflow | docker | 24.04.2 | 1/5
Your workflow is using a version of actions/cache that is scheduled for deprecation, actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9. Please update your workflow to use either v3 or v4 of actions/cache to avoid interruptions. Learn more: https://github.blog/changelog/2024-12-05-notice-of-upcoming-releases-and-breaking-changes-for-github-actions/#actions-cache-v1-v2-and-actions-toolkit-cache-package-closing-down
Test function | docker | latest-everything | 2/5
Your workflow is using a version of actions/cache that is scheduled for deprecation, actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9. Please update your workflow to use either v3 or v4 of actions/cache to avoid interruptions. Learn more: https://github.blog/changelog/2024-12-05-notice-of-upcoming-releases-and-breaking-changes-for-github-actions/#actions-cache-v1-v2-and-actions-toolkit-cache-package-closing-down
Test function | docker | latest-everything | 5/5
Your workflow is using a version of actions/cache that is scheduled for deprecation, actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9. Please update your workflow to use either v3 or v4 of actions/cache to avoid interruptions. Learn more: https://github.blog/changelog/2024-12-05-notice-of-upcoming-releases-and-breaking-changes-for-github-actions/#actions-cache-v1-v2-and-actions-toolkit-cache-package-closing-down
Test function | docker | latest-everything | 4/5
Your workflow is using a version of actions/cache that is scheduled for deprecation, actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9. Please update your workflow to use either v3 or v4 of actions/cache to avoid interruptions. Learn more: https://github.blog/changelog/2024-12-05-notice-of-upcoming-releases-and-breaking-changes-for-github-actions/#actions-cache-v1-v2-and-actions-toolkit-cache-package-closing-down
Test workflow | docker | 24.04.2 | 5/5
Your workflow is using a version of actions/cache that is scheduled for deprecation, actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9. Please update your workflow to use either v3 or v4 of actions/cache to avoid interruptions. Learn more: https://github.blog/changelog/2024-12-05-notice-of-upcoming-releases-and-breaking-changes-for-github-actions/#actions-cache-v1-v2-and-actions-toolkit-cache-package-closing-down
Test pipeline | docker | latest-everything | 3/5
Your workflow is using a version of actions/cache that is scheduled for deprecation, actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9. Please update your workflow to use either v3 or v4 of actions/cache to avoid interruptions. Learn more: https://github.blog/changelog/2024-12-05-notice-of-upcoming-releases-and-breaking-changes-for-github-actions/#actions-cache-v1-v2-and-actions-toolkit-cache-package-closing-down
Test pipeline | docker | latest-everything | 2/5
Your workflow is using a version of actions/cache that is scheduled for deprecation, actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9. Please update your workflow to use either v3 or v4 of actions/cache to avoid interruptions. Learn more: https://github.blog/changelog/2024-12-05-notice-of-upcoming-releases-and-breaking-changes-for-github-actions/#actions-cache-v1-v2-and-actions-toolkit-cache-package-closing-down
Test function | docker | latest-everything | 3/5
Your workflow is using a version of actions/cache that is scheduled for deprecation, actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9. Please update your workflow to use either v3 or v4 of actions/cache to avoid interruptions. Learn more: https://github.blog/changelog/2024-12-05-notice-of-upcoming-releases-and-breaking-changes-for-github-actions/#actions-cache-v1-v2-and-actions-toolkit-cache-package-closing-down
Test function | docker | latest-everything | 1/5
Your workflow is using a version of actions/cache that is scheduled for deprecation, actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9. Please update your workflow to use either v3 or v4 of actions/cache to avoid interruptions. Learn more: https://github.blog/changelog/2024-12-05-notice-of-upcoming-releases-and-breaking-changes-for-github-actions/#actions-cache-v1-v2-and-actions-toolkit-cache-package-closing-down
Test pipeline | docker | latest-everything | 4/5
Your workflow is using a version of actions/cache that is scheduled for deprecation, actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9. Please update your workflow to use either v3 or v4 of actions/cache to avoid interruptions. Learn more: https://github.blog/changelog/2024-12-05-notice-of-upcoming-releases-and-breaking-changes-for-github-actions/#actions-cache-v1-v2-and-actions-toolkit-cache-package-closing-down
Test pipeline | docker | latest-everything | 1/5
Your workflow is using a version of actions/cache that is scheduled for deprecation, actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9. Please update your workflow to use either v3 or v4 of actions/cache to avoid interruptions. Learn more: https://github.blog/changelog/2024-12-05-notice-of-upcoming-releases-and-breaking-changes-for-github-actions/#actions-cache-v1-v2-and-actions-toolkit-cache-package-closing-down
Test pipeline | docker | latest-everything | 5/5
Your workflow is using a version of actions/cache that is scheduled for deprecation, actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9. Please update your workflow to use either v3 or v4 of actions/cache to avoid interruptions. Learn more: https://github.blog/changelog/2024-12-05-notice-of-upcoming-releases-and-breaking-changes-for-github-actions/#actions-cache-v1-v2-and-actions-toolkit-cache-package-closing-down
Test workflow | docker | latest-everything | 2/5
Your workflow is using a version of actions/cache that is scheduled for deprecation, actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9. Please update your workflow to use either v3 or v4 of actions/cache to avoid interruptions. Learn more: https://github.blog/changelog/2024-12-05-notice-of-upcoming-releases-and-breaking-changes-for-github-actions/#actions-cache-v1-v2-and-actions-toolkit-cache-package-closing-down
Test workflow | docker | latest-everything | 5/5
Your workflow is using a version of actions/cache that is scheduled for deprecation, actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9. Please update your workflow to use either v3 or v4 of actions/cache to avoid interruptions. Learn more: https://github.blog/changelog/2024-12-05-notice-of-upcoming-releases-and-breaking-changes-for-github-actions/#actions-cache-v1-v2-and-actions-toolkit-cache-package-closing-down
Test workflow | docker | latest-everything | 4/5
Your workflow is using a version of actions/cache that is scheduled for deprecation, actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9. Please update your workflow to use either v3 or v4 of actions/cache to avoid interruptions. Learn more: https://github.blog/changelog/2024-12-05-notice-of-upcoming-releases-and-breaking-changes-for-github-actions/#actions-cache-v1-v2-and-actions-toolkit-cache-package-closing-down
Test workflow | docker | latest-everything | 3/5
Your workflow is using a version of actions/cache that is scheduled for deprecation, actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9. Please update your workflow to use either v3 or v4 of actions/cache to avoid interruptions. Learn more: https://github.blog/changelog/2024-12-05-notice-of-upcoming-releases-and-breaking-changes-for-github-actions/#actions-cache-v1-v2-and-actions-toolkit-cache-package-closing-down
Test workflow | docker | latest-everything | 1/5
Your workflow is using a version of actions/cache that is scheduled for deprecation, actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9. Please update your workflow to use either v3 or v4 of actions/cache to avoid interruptions. Learn more: https://github.blog/changelog/2024-12-05-notice-of-upcoming-releases-and-breaking-changes-for-github-actions/#actions-cache-v1-v2-and-actions-toolkit-cache-package-closing-down
0