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Merge pull request #1613 from lindenb/pl_goleft #6940

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Merge pull request #1613 from lindenb/pl_goleft

Merge pull request #1613 from lindenb/pl_goleft #6940

Triggered via push December 10, 2024 13:35
@FriederikeHanssenFriederikeHanssen
pushed 5c6be78
dev
Status Success
Total duration 5m 21s
Artifacts 1

linting.yml

on: push
pre-commit
16s
pre-commit
nf-core
2m 22s
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45 errors and 2 warnings
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 strelka --no_intervals | somatic: 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.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 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 | --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 | --tools controlfreec --no_intervals | tumoronly: Test pipeline#L1
Assertion failed: 1 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 | --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 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-mem --save_reference | skip QC/recal/md: Test pipeline#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline.Run with profile test | --aligner bwa-mem2 --save_reference --build_only_index: 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 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.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 | --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 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.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 strelka | somatic: 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 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
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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