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Add nf-test sharding CI #18

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Add nf-test sharding CI

Add nf-test sharding CI #18

Triggered via pull request October 4, 2024 07:46
@maxulyssemaxulysse
synchronize #1668
fresh-nf-test
Status Success
Total duration 19m 8s
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pytest.yml

on: pull_request
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346 errors
Test Workflow SAMPLESHEET_TO_CHANNEL.Should run without failures: Test Workflow SAMPLESHEET_TO_CHANNEL#L1
Assertion failed: assert workflow.success | | workflow false
Test Workflow UTILS_NFVALIDATION_PLUGIN.Should validate params: Test Workflow UTILS_NFVALIDATION_PLUGIN#L1
Assertion failed: 2 of 2 assertions failed
Test Workflow SAMPLESHEET_TO_CHANNEL.Should run without failures: Test Workflow SAMPLESHEET_TO_CHANNEL#L1
Assertion failed: assert workflow.success | | workflow false
Test Workflow UTILS_NFVALIDATION_PLUGIN.Should validate params: Test Workflow UTILS_NFVALIDATION_PLUGIN#L1
Assertion failed: 2 of 2 assertions failed
Test Process BCFTOOLS_ANNOTATE.sarscov2 - [vcf, [], annotation, annotation_tbi], [] - vcf_output: Test Process BCFTOOLS_ANNOTATE#L1
Assertion failed: 2 of 2 assertions failed
Test Process BCFTOOLS_ANNOTATE.sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - stub: Test Process BCFTOOLS_ANNOTATE#L1
Assertion failed: 2 of 2 assertions failed
Test Process BCFTOOLS_MPILEUP.sarscov2 - [bam, []], fasta, true: Test Process BCFTOOLS_MPILEUP#L1
Assertion failed: 5 of 6 assertions failed
Test Process BCFTOOLS_SORT.sarscov2 - vcf_gz_index: Test Process BCFTOOLS_SORT#L1
Assertion failed: 1 of 3 assertions failed
Test Process BCFTOOLS_SORT.sarscov2 - vcf_gz_index_csi - stub: Test Process BCFTOOLS_SORT#L1
Assertion failed: 1 of 3 assertions failed
Test Process BWA_MEM.Single-End Sort: Test Process BWA_MEM#L1
Assertion failed: 1 of 2 assertions failed
Test Process BWAMEM2_MEM.sarscov2 - [fastq1, fastq2], index, fasta, true: Test Process BWAMEM2_MEM#L1
Assertion failed: 1 of 2 assertions failed
Test Process CNVKIT_BATCH.cnvkit batch hybrid mode - bam: Test Process CNVKIT_BATCH#L1
java.lang.NullPointerException: Cannot invoke method getAt() on null object
Test Process CNVKIT_BATCH.cnvkit batch germline mode - cram: Test Process CNVKIT_BATCH#L1
Assertion failed: 1 of 2 assertions failed
Test Process CNVKIT_REFERENCE.human - [fasta, bed] - stub: Test Process CNVKIT_REFERENCE#L1
Assertion failed: 1 of 2 assertions failed
Test Process DRAGMAP_ALIGN.sarscov2 - fastq, hashtable, fasta, false: Test Process DRAGMAP_ALIGN#L1
Assertion failed: 1 of 2 assertions failed
Test Process DRAGMAP_ALIGN.sarscov2 - [fastq1, fastq2], hashtable, fasta, true - stub: Test Process DRAGMAP_ALIGN#L1
Assertion failed: 1 of 2 assertions failed
Test Process ENSEMBLVEP_VEP.test_ensemblvep_vep_fasta_vcf: Test Process ENSEMBLVEP_VEP#L1
Assertion failed: 2 of 3 assertions failed
Test Process FASTP.test_fastp_single_end_trim_fail: Test Process FASTP#L1
Assertion failed: 1 of 4 assertions failed
Test Process FASTP.test_fastp_paired_end_qc_only: Test Process FASTP#L1
Assertion failed: 2 of 4 assertions failed
Test Process FREEBAYES.sarscov2 - [ cram, crai ] - fasta - fai: Test Process FREEBAYES#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_APPLYBQSR.sarscov2 - cram: Test Process GATK4_APPLYBQSR#L1
Assertion failed: 1 of 3 assertions failed
Test Process GATK4_BASERECALIBRATOR.sarscov2 - bam - intervals: Test Process GATK4_BASERECALIBRATOR#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_ESTIMATELIBRARYCOMPLEXITY.homo_sapiens - bam: Test Process GATK4_ESTIMATELIBRARYCOMPLEXITY#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_GENOTYPEGVCFS.homo_sapiens - [gvcf_gz, tbi, [], []], fasta, fai, dict, dbsnp, dbsnp_tbi: Test Process GATK4_GENOTYPEGVCFS#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_HAPLOTYPECALLER.homo_sapiens - [cram, crai] - fasta - fai - dict - sites - sites_tbi: Test Process GATK4_HAPLOTYPECALLER#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4SPARK_APPLYBQSR.sarscov2 - bam intervals: Test Process GATK4SPARK_APPLYBQSR#L1
Assertion failed: 2 of 2 assertions failed
Test Process GATK4SPARK_MARKDUPLICATES.homo_sapiens - bam - metrics: Test Process GATK4SPARK_MARKDUPLICATES#L1
Assertion failed: 6 of 6 assertions failed
Test Process LOFREQ_CALLPARALLEL.sarscov2 - bam: Test Process LOFREQ_CALLPARALLEL#L1
Assertion failed: 1 of 2 assertions failed
Test Process MOSDEPTH.homo_sapiens - cram, crai, []: Test Process MOSDEPTH#L1
Assertion failed: 1 of 2 assertions failed
Test Process NGSCHECKMATE_NCM.sarscov2 - vcf - stub: Test Process NGSCHECKMATE_NCM#L1
Assertion failed: 2 of 2 assertions failed
Test Process SENTIEON_BWAMEM.Paired-End: Test Process SENTIEON_BWAMEM#L1
Assertion failed: 2 of 2 assertions failed
Test Process SENTIEON_DEDUP.Test stub: Test Process SENTIEON_DEDUP#L1
Assertion failed: 2 of 2 assertions failed
Test Process SENTIEON_GVCFTYPER.sentieon gvcftyper dbsnp intervals: Test Process SENTIEON_GVCFTYPER#L1
Assertion failed: 2 of 2 assertions failed
Test Process SENTIEON_HAPLOTYPER.Sentieon Haplotyper Intervals BOTH: Test Process SENTIEON_HAPLOTYPER#L1
Assertion failed: 2 of 2 assertions failed
Test Process SNPEFF_DOWNLOAD.test-snpeff-download: Test Process SNPEFF_DOWNLOAD#L1
Assertion failed: 1 of 2 assertions failed
Test Process STRELKA_SOMATIC.human - cram - stub: Test Process STRELKA_SOMATIC#L1
Assertion failed: 1 of 2 assertions failed
Test Process TIDDIT_SV.sarscov2 - bam - stub: Test Process TIDDIT_SV#L1
Assertion failed: 1 of 2 assertions failed
Test Process BCFTOOLS_ANNOTATE.sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_output: Test Process BCFTOOLS_ANNOTATE#L1
Assertion failed: 2 of 2 assertions failed
Test Process BCFTOOLS_ANNOTATE.sarscov2 - [vcf, [], annotation, annotation_tbi], header - bcf_output: Test Process BCFTOOLS_ANNOTATE#L1
Assertion failed: 2 of 2 assertions failed
Test Process BCFTOOLS_MPILEUP.sarscov2 - [bam, []], fasta, false stub: Test Process BCFTOOLS_MPILEUP#L1
Assertion failed: 4 of 5 assertions failed
Test Process BCFTOOLS_SORT.sarscov2 - vcf: Test Process BCFTOOLS_SORT#L1
Assertion failed: 1 of 2 assertions failed
Test Process BCFTOOLS_SORT.sarscov2 - vcf_gz_index - stub: Test Process BCFTOOLS_SORT#L1
Assertion failed: 1 of 3 assertions failed
Test Process BWA_MEM.Single-End: Test Process BWA_MEM#L1
Assertion failed: 1 of 2 assertions failed
Test Process BWAMEM2_MEM.sarscov2 - [fastq1, fastq2], index, fasta, false: Test Process BWAMEM2_MEM#L1
Assertion failed: 1 of 2 assertions failed
Test Process CNVKIT_ANTITARGET.human - bed - stub: Test Process CNVKIT_ANTITARGET#L1
Assertion failed: 1 of 2 assertions failed
Test Process CNVKIT_BATCH.cnvkit batch tumouronly mode - cram: Test Process CNVKIT_BATCH#L1
Assertion failed: 1 of 2 assertions failed
Test Process CNVKIT_REFERENCE.human - [fasta, bed]: Test Process CNVKIT_REFERENCE#L1
Assertion failed: 1 of 2 assertions failed
Test Process DEEPVARIANT_RUNDEEPVARIANT.homo_sapiens - [bam, bai] - fasta_gz - fasta_gz_fai: Test Process DEEPVARIANT_RUNDEEPVARIANT#L1
Assertion failed: 1 of 2 assertions failed
Test Process DRAGMAP_ALIGN.homo_sapiens - [fastq1, fastq2], hashtable, fasta, true: Test Process DRAGMAP_ALIGN#L1
Assertion failed: 1 of 2 assertions failed
Test Process ENSEMBLVEP_DOWNLOAD.celegans - download - stub: Test Process ENSEMBLVEP_DOWNLOAD#L1
Assertion failed: 1 of 2 assertions failed
Test Process FASTP.test_fastp_single_end_qc_only: Test Process FASTP#L1
Assertion failed: 1 of 4 assertions failed
Test Process FREEBAYES.sarscov2 - [ bam, bai, bed ] - fasta - fai: Test Process FREEBAYES#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_APPLYBQSR.sarscov2 - bam - intervals: Test Process GATK4_APPLYBQSR#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_BASERECALIBRATOR.sarscov2 - bam: Test Process GATK4_BASERECALIBRATOR#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_GENOTYPEGVCFS.homo_sapiens - [gvcf, idx, [], []], fasta, fai, dict, [], []: Test Process GATK4_GENOTYPEGVCFS#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_HAPLOTYPECALLER.homo_sapiens - [cram, crai] - fasta - fai - dict: Test Process GATK4_HAPLOTYPECALLER#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4SPARK_APPLYBQSR.sarscov2 - bam: Test Process GATK4SPARK_APPLYBQSR#L1
Assertion failed: 2 of 2 assertions failed
Test Process GATK4SPARK_MARKDUPLICATES.homo_sapiens - bam - multiple: Test Process GATK4SPARK_MARKDUPLICATES#L1
Assertion failed: 2 of 2 assertions failed
Test Process MOSDEPTH.homo_sapiens - bam, bai, bed: Test Process MOSDEPTH#L1
Assertion failed: 2 of 2 assertions failed
Test Process MOSDEPTH.homo_sapiens - bam, bai, bed - thresholds: Test Process MOSDEPTH#L1
Assertion failed: 2 of 2 assertions failed
Test Process NGSCHECKMATE_NCM.sarscov2 - bam - stub: Test Process NGSCHECKMATE_NCM#L1
Assertion failed: 2 of 2 assertions failed
Test Process SAMTOOLS_STATS.cram: Test Process SAMTOOLS_STATS#L1
Assertion failed: 1 of 2 assertions failed
Test Process SENTIEON_BWAMEM.Single-End Output CRAM: Test Process SENTIEON_BWAMEM#L1
Assertion failed: 2 of 2 assertions failed
Test Process SENTIEON_DEDUP.Test removing duplicates: Test Process SENTIEON_DEDUP#L1
Assertion failed: 2 of 2 assertions failed
Test Process SENTIEON_GVCFTYPER.sentieon gvcftyper intervals: Test Process SENTIEON_GVCFTYPER#L1
Assertion failed: 2 of 2 assertions failed
Test Process SENTIEON_HAPLOTYPER.Sentieon Haplotyper BOTH: Test Process SENTIEON_HAPLOTYPER#L1
Assertion failed: 2 of 2 assertions failed
Test Process SENTIEON_HAPLOTYPER.Sentieon Haplotyper - stub: Test Process SENTIEON_HAPLOTYPER#L1
Assertion failed: 2 of 2 assertions failed
Test Process SPRING_DECOMPRESS.Write-Two-Files: Test Process SPRING_DECOMPRESS#L1
Assertion failed: 2 of 2 assertions failed
Test Process TIDDIT_SV.human - cram - no_bwa: Test Process TIDDIT_SV#L1
Assertion failed: 3 of 4 assertions failed
Test Process BCFTOOLS_ANNOTATE.sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index: Test Process BCFTOOLS_ANNOTATE#L1
Assertion failed: 3 of 3 assertions failed
Test Process BCFTOOLS_ANNOTATE.sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index - stub: Test Process BCFTOOLS_ANNOTATE#L1
Assertion failed: 3 of 3 assertions failed
Test Process BCFTOOLS_MPILEUP.sarscov2 - [bam, []], fasta, true stub: Test Process BCFTOOLS_MPILEUP#L1
Assertion failed: 5 of 6 assertions failed
Test Process BCFTOOLS_SORT.sarscov2 - vcf_gz_index_csi: Test Process BCFTOOLS_SORT#L1
Assertion failed: 1 of 3 assertions failed
Test Process BCFTOOLS_SORT.sarscov2 - vcf_gz_index_tbi - stub: Test Process BCFTOOLS_SORT#L1
Assertion failed: 1 of 3 assertions failed
Test Process BWA_MEM.Paired-End: Test Process BWA_MEM#L1
Assertion failed: 1 of 2 assertions failed
Test Process BWAMEM2_INDEX.BWAMEM2 index: Test Process BWAMEM2_INDEX#L1
Assertion failed: 1 of 2 assertions failed
Test Process BWAMEM2_MEM.sarscov2 - [fastq1, fastq2], index, fasta, true - stub: Test Process BWAMEM2_MEM#L1
Assertion failed: 1 of 2 assertions failed
Test Process CNVKIT_BATCH.cnvkit batch wgs - bam: Test Process CNVKIT_BATCH#L1
Assertion failed: 1 of 2 assertions failed
Test Process CNVKIT_BATCH.cnvkit batch germline hybrid mode - bam: Test Process CNVKIT_BATCH#L1
Assertion failed: 1 of 2 assertions failed
Test Process CONTROLFREEC_ASSESSSIGNIFICANCE.human - freec_ratio: Test Process CONTROLFREEC_ASSESSSIGNIFICANCE#L1
Assertion failed: 1 of 3 assertions failed
Test Process DEEPVARIANT_RUNDEEPVARIANT.homo_sapiens - [bam, bai] - fasta - fai: Test Process DEEPVARIANT_RUNDEEPVARIANT#L1
Assertion failed: 1 of 2 assertions failed
Test Process DRAGMAP_ALIGN.sarscov2 - fastq, hashtable, fasta, true: Test Process DRAGMAP_ALIGN#L1
Assertion failed: 1 of 2 assertions failed
Test Process DRAGMAP_HASHTABLE.sarscov2 - fasta: Test Process DRAGMAP_HASHTABLE#L1
Assertion failed: 1 of 2 assertions failed
Test Process ENSEMBLVEP_VEP.test_ensemblvep_vep_fasta_tab_gz: Test Process ENSEMBLVEP_VEP#L1
Assertion failed: 2 of 3 assertions failed
Test Process FREEBAYES.sarscov2 - [ bam, bai, bam, bai ] - fasta - fai: Test Process FREEBAYES#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_BASERECALIBRATOR.sarscov2 - bam - multiple sites: Test Process GATK4_BASERECALIBRATOR#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_ESTIMATELIBRARYCOMPLEXITY.homo_sapiens - cram: Test Process GATK4_ESTIMATELIBRARYCOMPLEXITY#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_GENOMICSDBIMPORT.test_gatk4_genomicsdbimport_get_intervalslist: Test Process GATK4_GENOMICSDBIMPORT#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_GENOTYPEGVCFS.homo_sapiens - [gvcf_gz, tbi, bed, []], fasta, fai, dict, [], []: Test Process GATK4_GENOTYPEGVCFS#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_HAPLOTYPECALLER.homo_sapiens - [cram, crai, dragstr_model] - fasta - fai - dict - sites - sites_tbi: Test Process GATK4_HAPLOTYPECALLER#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4SPARK_APPLYBQSR.sarscov2 - bam - stub: Test Process GATK4SPARK_APPLYBQSR#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4SPARK_MARKDUPLICATES.homo_sapiens - cram: Test Process GATK4SPARK_MARKDUPLICATES#L1
Assertion failed: 2 of 2 assertions failed
Test Process LOFREQ_CALLPARALLEL.sarscov2 - bam - bed: Test Process LOFREQ_CALLPARALLEL#L1
Assertion failed: 1 of 2 assertions failed
Test Process MANTA_TUMORONLY.human - cram - bed: Test Process MANTA_TUMORONLY#L1
Assertion failed: 1 of 5 assertions failed
Test Process MOSDEPTH.homo_sapiens - cram, crai, bed: Test Process MOSDEPTH#L1
Assertion failed: 2 of 2 assertions failed
Test Process MOSDEPTH.homo_sapiens - bam, bai, [] - stub: Test Process MOSDEPTH#L1
Assertion failed: 1 of 2 assertions failed
Test Process SAMBLASTER.homo_sapiens-test_paired_end_umi_unsorted_bam: Test Process SAMBLASTER#L1
Assertion failed: 1 of 2 assertions failed
Test Process SAMTOOLS_MPILEUP.bam_bed: Test Process SAMTOOLS_MPILEUP#L1
Assertion failed: 2 of 3 assertions failed
Test Process SENTIEON_BWAMEM.Single-End - stub: Test Process SENTIEON_BWAMEM#L1
Assertion failed: 2 of 2 assertions failed
Test Process SENTIEON_GVCFTYPER.sentieon gvcftyper vcf: Test Process SENTIEON_GVCFTYPER#L1
Assertion failed: 2 of 2 assertions failed
Test Process SENTIEON_GVCFTYPER.sentieon gvcftyper - stub: Test Process SENTIEON_GVCFTYPER#L1
Assertion failed: 2 of 2 assertions failed
Test Process SENTIEON_HAPLOTYPER.Sentieon Haplotyper DBSNP BOTH: Test Process SENTIEON_HAPLOTYPER#L1
Assertion failed: 2 of 2 assertions failed
Test Process SNPEFF_DOWNLOAD.test-snpeff-download-stub: Test Process SNPEFF_DOWNLOAD#L1
Assertion failed: 1 of 2 assertions failed
Test Process TIDDIT_SV.sarscov2 - bam - bwa: Test Process TIDDIT_SV#L1
Assertion failed: 3 of 4 assertions failed
Test Process BCFTOOLS_ANNOTATE.sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_csi: Test Process BCFTOOLS_ANNOTATE#L1
Assertion failed: 3 of 3 assertions failed
Test Process BCFTOOLS_ANNOTATE.sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_csi - stub: Test Process BCFTOOLS_ANNOTATE#L1
Assertion failed: 3 of 3 assertions failed
Test Process BCFTOOLS_MPILEUP.sarscov2 - [bam, bed], fasta, false: Test Process BCFTOOLS_MPILEUP#L1
Assertion failed: 4 of 5 assertions failed
Test Process BCFTOOLS_SORT.sarscov2 - vcf_gz_index_tbi: Test Process BCFTOOLS_SORT#L1
Assertion failed: 1 of 3 assertions failed
Test Process BWA_MEM.Paired-End Sort: Test Process BWA_MEM#L1
Assertion failed: 1 of 2 assertions failed
Test Process BWAMEM2_MEM.sarscov2 - fastq, index, fasta, false: Test Process BWAMEM2_MEM#L1
Assertion failed: 1 of 2 assertions failed
Test Process CNVKIT_BATCH.cnvkit batch wgs - cram: Test Process CNVKIT_BATCH#L1
Assertion failed: 1 of 2 assertions failed
Test Process CNVKIT_BATCH.cnvkit batch pon mode - bam: Test Process CNVKIT_BATCH#L1
Assertion failed: 1 of 2 assertions failed
Test Process CNVKIT_GENEMETRICS.test-cnvkit-genemetrics-with-cns: Test Process CNVKIT_GENEMETRICS#L1
Assertion failed: 1 of 2 assertions failed
Test Process CONTROLFREEC_ASSESSSIGNIFICANCE.human - freec_ratio - stub: Test Process CONTROLFREEC_ASSESSSIGNIFICANCE#L1
Assertion failed: 1 of 2 assertions failed
Test Process DEEPVARIANT_RUNDEEPVARIANT.homo_sapiens - [cram, crai, genome_bed] - fasta - fai: Test Process DEEPVARIANT_RUNDEEPVARIANT#L1
Assertion failed: 1 of 2 assertions failed
Test Process DRAGMAP_ALIGN.sarscov2 - [fastq1, fastq2], hashtable, fasta, false: Test Process DRAGMAP_ALIGN#L1
Assertion failed: 1 of 2 assertions failed
Test Process DRAGMAP_HASHTABLE.sarscov2 - fasta - stub: Test Process DRAGMAP_HASHTABLE#L1
Assertion failed: 1 of 2 assertions failed
Test Process FASTP.test_fastp_single_end: Test Process FASTP#L1
Assertion failed: 1 of 4 assertions failed
Test Process FASTP.test_fastp_paired_end_merged: Test Process FASTP#L1
Assertion failed: 2 of 4 assertions failed
Test Process FGBIO_CALLMOLECULARCONSENSUSREADS.homo_sapiens - bam: Test Process FGBIO_CALLMOLECULARCONSENSUSREADS#L1
Assertion failed: 2 of 2 assertions failed
Test Process FREEBAYES.sarscov2 - [ cram, crai, cram, crai, bed ] - fasta - fai: Test Process FREEBAYES#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_BASERECALIBRATOR.sarscov2 - bam - stub: Test Process GATK4_BASERECALIBRATOR#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_ESTIMATELIBRARYCOMPLEXITY.sarscov2 - bam - stub: Test Process GATK4_ESTIMATELIBRARYCOMPLEXITY#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_GATHERBQSRREPORTS.test-gatk4-gatherbqsrreports: Test Process GATK4_GATHERBQSRREPORTS#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_GENOTYPEGVCFS.homo_sapiens - [gendb, [], [], []], fasta, fai, dict, [], []: Test Process GATK4_GENOTYPEGVCFS#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4SPARK_APPLYBQSR.sarscov2 - cram: Test Process GATK4SPARK_APPLYBQSR#L1
Assertion failed: 2 of 2 assertions failed
Test Process MOSDEPTH.homo_sapiens - bam, bai, [] - window: Test Process MOSDEPTH#L1
Assertion failed: 1 of 2 assertions failed
Test Process MSISENSORPRO_SCAN.test-msisensorpro-scan: Test Process MSISENSORPRO_SCAN#L1
Assertion failed: 1 of 2 assertions failed
Test Process NGSCHECKMATE_NCM.sarscov2 - bam: Test Process NGSCHECKMATE_NCM#L1
Assertion failed: 2 of 2 assertions failed
Test Process SAMBLASTER.stub: Test Process SAMBLASTER#L1
Assertion failed: 1 of 2 assertions failed
Test Process SAMTOOLS_MPILEUP.bam_bed_fasta: Test Process SAMTOOLS_MPILEUP#L1
Assertion failed: 2 of 3 assertions failed
Test Process SENTIEON_BWAMEM.Paired-End - stub: Test Process SENTIEON_BWAMEM#L1
Assertion failed: 2 of 2 assertions failed
Test Process SENTIEON_GVCFTYPER.sentieon gvcftyper vcf.gz: Test Process SENTIEON_GVCFTYPER#L1
Assertion failed: 2 of 2 assertions failed
Test Process SENTIEON_HAPLOTYPER.Sentieon Haplotyper VCF: Test Process SENTIEON_HAPLOTYPER#L1
Assertion failed: 2 of 2 assertions failed
Test Process SENTIEON_HAPLOTYPER.Sentieon Haplotyper Recalibration: Test Process SENTIEON_HAPLOTYPER#L1
Assertion failed: 2 of 2 assertions failed
Test Process SNPEFF_SNPEFF.test_SNPEFF_SNPEFF: Test Process SNPEFF_SNPEFF#L1
Assertion failed: 5 of 6 assertions failed
Test Process STRELKA_GERMLINE.human - cram - stub: Test Process STRELKA_GERMLINE#L1
Assertion failed: 1 of 2 assertions failed
Test Process TIDDIT_SV.sarscov2 - bam - no_bwa: Test Process TIDDIT_SV#L1
Assertion failed: 3 of 4 assertions failed
Test Process BCFTOOLS_ANNOTATE.sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_tbi: Test Process BCFTOOLS_ANNOTATE#L1
Assertion failed: 3 of 3 assertions failed
Test Process BCFTOOLS_ANNOTATE.sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_tbi - stub: Test Process BCFTOOLS_ANNOTATE#L1
Assertion failed: 3 of 3 assertions failed
Test Process BCFTOOLS_MPILEUP.sarscov2 - [bam, []], fasta, false: Test Process BCFTOOLS_MPILEUP#L1
Assertion failed: 4 of 5 assertions failed
Test Process BCFTOOLS_MPILEUP.sarscov2 - [bam, bed], fasta, false stub: Test Process BCFTOOLS_MPILEUP#L1
Assertion failed: 4 of 5 assertions failed
Test Process BCFTOOLS_SORT.sarscov2 - vcf - stub: Test Process BCFTOOLS_SORT#L1
Assertion failed: 1 of 2 assertions failed
Test Process BWA_MEM.Paired-End - no fasta: Test Process BWA_MEM#L1
Assertion failed: 1 of 2 assertions failed
Test Process BWAMEM2_MEM.sarscov2 - fastq, index, fasta, true: Test Process BWAMEM2_MEM#L1
Assertion failed: 1 of 2 assertions failed
Test Process CNVKIT_ANTITARGET.human - bed: Test Process CNVKIT_ANTITARGET#L1
Assertion failed: 1 of 2 assertions failed
Test Process CNVKIT_BATCH.cnvkit batch tumouronly mode - bam: Test Process CNVKIT_BATCH#L1
Assertion failed: 1 of 2 assertions failed
Test Process CNVKIT_BATCH.cnvkit batch - bam - stub: Test Process CNVKIT_BATCH#L1
Assertion failed: 1 of 2 assertions failed
Test Process CNVKIT_GENEMETRICS.test-cnvkit-genemetrics-without-cns: Test Process CNVKIT_GENEMETRICS#L1
Assertion failed: 1 of 2 assertions failed
Test Process DEEPVARIANT_RUNDEEPVARIANT.homo_sapiens - [cram, crai, genome_bed] - fasta - fai - par_bed: Test Process DEEPVARIANT_RUNDEEPVARIANT#L1
Assertion failed: 1 of 2 assertions failed
Test Process DRAGMAP_ALIGN.sarscov2 - [fastq1, fastq2], hashtable, fasta, true: Test Process DRAGMAP_ALIGN#L1
Assertion failed: 1 of 2 assertions failed
Test Process ENSEMBLVEP_DOWNLOAD.celegans - download: Test Process ENSEMBLVEP_DOWNLOAD#L1
Assertion failed: 1 of 2 assertions failed
Test Process FASTP.test_fastp_paired_end: Test Process FASTP#L1
Assertion failed: 2 of 4 assertions failed
Test Process FASTP.test_fastp_paired_end_merged_adapterlist: Test Process FASTP#L1
Assertion failed: 1 of 4 assertions failed
Test Process FGBIO_CALLMOLECULARCONSENSUSREADS.homo_sapiens - stub: Test Process FGBIO_CALLMOLECULARCONSENSUSREADS#L1
Assertion failed: 2 of 2 assertions failed
Test Process FREEBAYES.sarscov2 - [ bam, bai ] - fasta - fai: Test Process FREEBAYES#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_APPLYBQSR.sarscov2 - bam: Test Process GATK4_APPLYBQSR#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_BASERECALIBRATOR.homo_sapiens - cram : Test Process GATK4_BASERECALIBRATOR#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_GATHERBQSRREPORTS.test-gatk4-gatherbqsrreports-multiple: Test Process GATK4_GATHERBQSRREPORTS#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_GENOMICSDBIMPORT.test_gatk4_genomicsdbimport_stub: Test Process GATK4_GENOMICSDBIMPORT#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_GENOTYPEGVCFS.homo_sapiens - [gendb, bed, [], []], fasta, fai, dict, [], []: Test Process GATK4_GENOTYPEGVCFS#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_HAPLOTYPECALLER.homo_sapiens - [bam, bai] - fasta - fai - dict: Test Process GATK4_HAPLOTYPECALLER#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4SPARK_MARKDUPLICATES.sarscov2 - bam: Test Process GATK4SPARK_MARKDUPLICATES#L1
Assertion failed: 2 of 2 assertions failed
Test Process MOSDEPTH.homo_sapiens - bam, bai, []: Test Process MOSDEPTH#L1
Assertion failed: 1 of 2 assertions failed
Test Process MOSDEPTH.homo_sapiens - bam, bai, [] - quantized: Test Process MOSDEPTH#L1
Assertion failed: 1 of 2 assertions failed
Test Process MSISENSORPRO_SCAN.test-msisensorpro-scan-stub: Test Process MSISENSORPRO_SCAN#L1
Assertion failed: 1 of 2 assertions failed
Test Process NGSCHECKMATE_NCM.sarscov2 - vcf: Test Process NGSCHECKMATE_NCM#L1
Assertion failed: 2 of 2 assertions failed
Test Process SAMTOOLS_STATS.bam: Test Process SAMTOOLS_STATS#L1
Assertion failed: 1 of 2 assertions failed
Test Process SENTIEON_BWAMEM.Single-End: Test Process SENTIEON_BWAMEM#L1
Assertion failed: 2 of 2 assertions failed
Test Process SENTIEON_DEDUP.Test marking duplicates: Test Process SENTIEON_DEDUP#L1
Assertion failed: 2 of 2 assertions failed
Test Process SENTIEON_GVCFTYPER.sentieon gvcftyper dbsnp: Test Process SENTIEON_GVCFTYPER#L1
Assertion failed: 2 of 2 assertions failed
Test Process SENTIEON_HAPLOTYPER.Sentieon Haplotyper GVCF: Test Process SENTIEON_HAPLOTYPER#L1
Assertion failed: 2 of 2 assertions failed
Test Process SENTIEON_HAPLOTYPER.Sentieon Haplotyper multiple CRAMs: Test Process SENTIEON_HAPLOTYPER#L1
Assertion failed: 2 of 2 assertions failed
Test Process SPRING_DECOMPRESS.Write-One-File: Test Process SPRING_DECOMPRESS#L1
Assertion failed: 2 of 2 assertions failed
Test Process TIDDIT_SV.human - cram - bwa: Test Process TIDDIT_SV#L1
Assertion failed: 3 of 4 assertions failed
Test Process BCFTOOLS_ANNOTATE.sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_csi: Test Process BCFTOOLS_ANNOTATE#L1
Assertion failed: 3 of 3 assertions failed
Test Process BCFTOOLS_ANNOTATE.sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_csi - stub: Test Process BCFTOOLS_ANNOTATE#L1
Assertion failed: 3 of 3 assertions failed
Test Process BCFTOOLS_MPILEUP.sarscov2 - [bam, bed], fasta, false: Test Process BCFTOOLS_MPILEUP#L1
Assertion failed: 4 of 5 assertions failed
Test Process BCFTOOLS_SORT.sarscov2 - vcf_gz_index_tbi: Test Process BCFTOOLS_SORT#L1
Assertion failed: 1 of 3 assertions failed
Test Process BWA_MEM.Paired-End Sort: Test Process BWA_MEM#L1
Assertion failed: 1 of 2 assertions failed
Test Process BWAMEM2_MEM.sarscov2 - fastq, index, fasta, false: Test Process BWAMEM2_MEM#L1
Assertion failed: 1 of 2 assertions failed
Test Process CNVKIT_BATCH.cnvkit batch wgs - cram: Test Process CNVKIT_BATCH#L1
Assertion failed: 1 of 2 assertions failed
Test Process CNVKIT_BATCH.cnvkit batch pon mode - bam: Test Process CNVKIT_BATCH#L1
Assertion failed: 1 of 2 assertions failed
Test Process CNVKIT_GENEMETRICS.test-cnvkit-genemetrics-with-cns: Test Process CNVKIT_GENEMETRICS#L1
Assertion failed: 1 of 2 assertions failed
Test Process CONTROLFREEC_ASSESSSIGNIFICANCE.human - freec_ratio - stub: Test Process CONTROLFREEC_ASSESSSIGNIFICANCE#L1
Assertion failed: 1 of 2 assertions failed
Test Process DEEPVARIANT_RUNDEEPVARIANT.homo_sapiens - [cram, crai, genome_bed] - fasta - fai: Test Process DEEPVARIANT_RUNDEEPVARIANT#L1
Assertion failed: 1 of 2 assertions failed
Test Process DRAGMAP_ALIGN.sarscov2 - [fastq1, fastq2], hashtable, fasta, false: Test Process DRAGMAP_ALIGN#L1
Assertion failed: 1 of 2 assertions failed
Test Process DRAGMAP_HASHTABLE.sarscov2 - fasta - stub: Test Process DRAGMAP_HASHTABLE#L1
Assertion failed: 1 of 2 assertions failed
Test Process FASTP.test_fastp_single_end: Test Process FASTP#L1
Assertion failed: 1 of 4 assertions failed
Test Process FASTP.test_fastp_paired_end_merged: Test Process FASTP#L1
Assertion failed: 2 of 4 assertions failed
Test Process FGBIO_CALLMOLECULARCONSENSUSREADS.homo_sapiens - bam: Test Process FGBIO_CALLMOLECULARCONSENSUSREADS#L1
Assertion failed: 2 of 2 assertions failed
Test Process FREEBAYES.sarscov2 - [ cram, crai, cram, crai, bed ] - fasta - fai: Test Process FREEBAYES#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_BASERECALIBRATOR.sarscov2 - bam - stub: Test Process GATK4_BASERECALIBRATOR#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_ESTIMATELIBRARYCOMPLEXITY.sarscov2 - bam - stub: Test Process GATK4_ESTIMATELIBRARYCOMPLEXITY#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_GATHERBQSRREPORTS.test-gatk4-gatherbqsrreports: Test Process GATK4_GATHERBQSRREPORTS#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_GENOTYPEGVCFS.homo_sapiens - [gendb, [], [], []], fasta, fai, dict, [], []: Test Process GATK4_GENOTYPEGVCFS#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4SPARK_APPLYBQSR.sarscov2 - cram: Test Process GATK4SPARK_APPLYBQSR#L1
Assertion failed: 2 of 2 assertions failed
Test Process MOSDEPTH.homo_sapiens - bam, bai, [] - window: Test Process MOSDEPTH#L1
Assertion failed: 1 of 2 assertions failed
Test Process MSISENSORPRO_SCAN.test-msisensorpro-scan: Test Process MSISENSORPRO_SCAN#L1
Assertion failed: 1 of 2 assertions failed
Test Process NGSCHECKMATE_NCM.sarscov2 - bam: Test Process NGSCHECKMATE_NCM#L1
Assertion failed: 2 of 2 assertions failed
Test Process SAMBLASTER.stub: Test Process SAMBLASTER#L1
Assertion failed: 1 of 2 assertions failed
Test Process SAMTOOLS_MPILEUP.bam_bed_fasta: Test Process SAMTOOLS_MPILEUP#L1
Assertion failed: 2 of 3 assertions failed
Test Process SENTIEON_BWAMEM.Paired-End - stub: Test Process SENTIEON_BWAMEM#L1
Assertion failed: 2 of 2 assertions failed
Test Process SENTIEON_GVCFTYPER.sentieon gvcftyper vcf.gz: Test Process SENTIEON_GVCFTYPER#L1
Assertion failed: 2 of 2 assertions failed
Test Process SENTIEON_HAPLOTYPER.Sentieon Haplotyper VCF: Test Process SENTIEON_HAPLOTYPER#L1
Assertion failed: 2 of 2 assertions failed
Test Process SENTIEON_HAPLOTYPER.Sentieon Haplotyper Recalibration: Test Process SENTIEON_HAPLOTYPER#L1
Assertion failed: 2 of 2 assertions failed
Test Process SNPEFF_SNPEFF.test_SNPEFF_SNPEFF: Test Process SNPEFF_SNPEFF#L1
Assertion failed: 5 of 6 assertions failed
Test Process STRELKA_GERMLINE.human - cram - stub: Test Process STRELKA_GERMLINE#L1
Assertion failed: 1 of 2 assertions failed
Test Process TIDDIT_SV.sarscov2 - bam - no_bwa: Test Process TIDDIT_SV#L1
Assertion failed: 3 of 4 assertions failed
Test Process BCFTOOLS_ANNOTATE.sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_tbi: Test Process BCFTOOLS_ANNOTATE#L1
Assertion failed: 3 of 3 assertions failed
Test Process BCFTOOLS_ANNOTATE.sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_tbi - stub: Test Process BCFTOOLS_ANNOTATE#L1
Assertion failed: 3 of 3 assertions failed
Test Process BCFTOOLS_MPILEUP.sarscov2 - [bam, []], fasta, false: Test Process BCFTOOLS_MPILEUP#L1
Assertion failed: 4 of 5 assertions failed
Test Process BCFTOOLS_MPILEUP.sarscov2 - [bam, bed], fasta, false stub: Test Process BCFTOOLS_MPILEUP#L1
Assertion failed: 4 of 5 assertions failed
Test Process BCFTOOLS_SORT.sarscov2 - vcf - stub: Test Process BCFTOOLS_SORT#L1
Assertion failed: 1 of 2 assertions failed
Test Process BWA_MEM.Paired-End - no fasta: Test Process BWA_MEM#L1
Assertion failed: 1 of 2 assertions failed
Test Process BWAMEM2_MEM.sarscov2 - fastq, index, fasta, true: Test Process BWAMEM2_MEM#L1
Assertion failed: 1 of 2 assertions failed
Test Process CNVKIT_ANTITARGET.human - bed: Test Process CNVKIT_ANTITARGET#L1
Assertion failed: 1 of 2 assertions failed
Test Process CNVKIT_BATCH.cnvkit batch tumouronly mode - bam: Test Process CNVKIT_BATCH#L1
Assertion failed: 1 of 2 assertions failed
Test Process CNVKIT_BATCH.cnvkit batch - bam - stub: Test Process CNVKIT_BATCH#L1
Assertion failed: 1 of 2 assertions failed
Test Process CNVKIT_GENEMETRICS.test-cnvkit-genemetrics-without-cns: Test Process CNVKIT_GENEMETRICS#L1
Assertion failed: 1 of 2 assertions failed
Test Process DEEPVARIANT_RUNDEEPVARIANT.homo_sapiens - [cram, crai, genome_bed] - fasta - fai - par_bed: Test Process DEEPVARIANT_RUNDEEPVARIANT#L1
Assertion failed: 1 of 2 assertions failed
Test Process DRAGMAP_ALIGN.sarscov2 - [fastq1, fastq2], hashtable, fasta, true: Test Process DRAGMAP_ALIGN#L1
Assertion failed: 1 of 2 assertions failed
Test Process ENSEMBLVEP_DOWNLOAD.celegans - download: Test Process ENSEMBLVEP_DOWNLOAD#L1
Assertion failed: 1 of 2 assertions failed
Test Process FASTP.test_fastp_paired_end: Test Process FASTP#L1
Assertion failed: 2 of 4 assertions failed
Test Process FASTP.test_fastp_paired_end_merged_adapterlist: Test Process FASTP#L1
Assertion failed: 1 of 4 assertions failed
Test Process FGBIO_CALLMOLECULARCONSENSUSREADS.homo_sapiens - stub: Test Process FGBIO_CALLMOLECULARCONSENSUSREADS#L1
Assertion failed: 2 of 2 assertions failed
Test Process FREEBAYES.sarscov2 - [ bam, bai ] - fasta - fai: Test Process FREEBAYES#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_APPLYBQSR.sarscov2 - bam: Test Process GATK4_APPLYBQSR#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_BASERECALIBRATOR.homo_sapiens - cram : Test Process GATK4_BASERECALIBRATOR#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_GATHERBQSRREPORTS.test-gatk4-gatherbqsrreports-multiple: Test Process GATK4_GATHERBQSRREPORTS#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_GENOMICSDBIMPORT.test_gatk4_genomicsdbimport_stub: Test Process GATK4_GENOMICSDBIMPORT#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_GENOTYPEGVCFS.homo_sapiens - [gendb, bed, [], []], fasta, fai, dict, [], []: Test Process GATK4_GENOTYPEGVCFS#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_HAPLOTYPECALLER.homo_sapiens - [bam, bai] - fasta - fai - dict: Test Process GATK4_HAPLOTYPECALLER#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4SPARK_MARKDUPLICATES.sarscov2 - bam: Test Process GATK4SPARK_MARKDUPLICATES#L1
Assertion failed: 2 of 2 assertions failed
Test Process MOSDEPTH.homo_sapiens - bam, bai, []: Test Process MOSDEPTH#L1
Assertion failed: 1 of 2 assertions failed
Test Process MOSDEPTH.homo_sapiens - bam, bai, [] - quantized: Test Process MOSDEPTH#L1
Assertion failed: 1 of 2 assertions failed
Test Process MSISENSORPRO_SCAN.test-msisensorpro-scan-stub: Test Process MSISENSORPRO_SCAN#L1
Assertion failed: 1 of 2 assertions failed
Test Process NGSCHECKMATE_NCM.sarscov2 - vcf: Test Process NGSCHECKMATE_NCM#L1
Assertion failed: 2 of 2 assertions failed
Test Process SAMTOOLS_STATS.bam: Test Process SAMTOOLS_STATS#L1
Assertion failed: 1 of 2 assertions failed
Test Process SENTIEON_BWAMEM.Single-End: Test Process SENTIEON_BWAMEM#L1
Assertion failed: 2 of 2 assertions failed
Test Process SENTIEON_DEDUP.Test marking duplicates: Test Process SENTIEON_DEDUP#L1
Assertion failed: 2 of 2 assertions failed
Test Process SENTIEON_GVCFTYPER.sentieon gvcftyper dbsnp: Test Process SENTIEON_GVCFTYPER#L1
Assertion failed: 2 of 2 assertions failed
Test Process SENTIEON_HAPLOTYPER.Sentieon Haplotyper GVCF: Test Process SENTIEON_HAPLOTYPER#L1
Assertion failed: 2 of 2 assertions failed
Test Process SENTIEON_HAPLOTYPER.Sentieon Haplotyper multiple CRAMs: Test Process SENTIEON_HAPLOTYPER#L1
Assertion failed: 2 of 2 assertions failed
Test Process SPRING_DECOMPRESS.Write-One-File: Test Process SPRING_DECOMPRESS#L1
Assertion failed: 2 of 2 assertions failed
Test Process TIDDIT_SV.human - cram - bwa: Test Process TIDDIT_SV#L1
Assertion failed: 3 of 4 assertions failed
Test Process BCFTOOLS_ANNOTATE.sarscov2 - [vcf, [], annotation, annotation_tbi], [] - vcf_output: Test Process BCFTOOLS_ANNOTATE#L1
Assertion failed: 2 of 2 assertions failed
Test Process BCFTOOLS_ANNOTATE.sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - stub: Test Process BCFTOOLS_ANNOTATE#L1
Assertion failed: 2 of 2 assertions failed
Test Process BCFTOOLS_MPILEUP.sarscov2 - [bam, []], fasta, true: Test Process BCFTOOLS_MPILEUP#L1
Assertion failed: 5 of 6 assertions failed
Test Process BCFTOOLS_SORT.sarscov2 - vcf_gz_index: Test Process BCFTOOLS_SORT#L1
Assertion failed: 1 of 3 assertions failed
Test Process BCFTOOLS_SORT.sarscov2 - vcf_gz_index_csi - stub: Test Process BCFTOOLS_SORT#L1
Assertion failed: 1 of 3 assertions failed
Test Process BWA_MEM.Single-End Sort: Test Process BWA_MEM#L1
Assertion failed: 1 of 2 assertions failed
Test Process BWAMEM2_MEM.sarscov2 - [fastq1, fastq2], index, fasta, true: Test Process BWAMEM2_MEM#L1
Assertion failed: 1 of 2 assertions failed
Test Process CNVKIT_BATCH.cnvkit batch hybrid mode - bam: Test Process CNVKIT_BATCH#L1
java.lang.NullPointerException: Cannot invoke method getAt() on null object
Test Process CNVKIT_BATCH.cnvkit batch germline mode - cram: Test Process CNVKIT_BATCH#L1
Assertion failed: 1 of 2 assertions failed
Test Process CNVKIT_REFERENCE.human - [fasta, bed] - stub: Test Process CNVKIT_REFERENCE#L1
Assertion failed: 1 of 2 assertions failed
Test Process DRAGMAP_ALIGN.sarscov2 - fastq, hashtable, fasta, false: Test Process DRAGMAP_ALIGN#L1
Assertion failed: 1 of 2 assertions failed
Test Process DRAGMAP_ALIGN.sarscov2 - [fastq1, fastq2], hashtable, fasta, true - stub: Test Process DRAGMAP_ALIGN#L1
Assertion failed: 1 of 2 assertions failed
Test Process ENSEMBLVEP_VEP.test_ensemblvep_vep_fasta_vcf: Test Process ENSEMBLVEP_VEP#L1
Assertion failed: 2 of 3 assertions failed
Test Process FASTP.test_fastp_single_end_trim_fail: Test Process FASTP#L1
Assertion failed: 1 of 4 assertions failed
Test Process FASTP.test_fastp_paired_end_qc_only: Test Process FASTP#L1
Assertion failed: 2 of 4 assertions failed
Test Process FREEBAYES.sarscov2 - [ cram, crai ] - fasta - fai: Test Process FREEBAYES#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_APPLYBQSR.sarscov2 - cram: Test Process GATK4_APPLYBQSR#L1
Assertion failed: 1 of 3 assertions failed
Test Process GATK4_BASERECALIBRATOR.sarscov2 - bam - intervals: Test Process GATK4_BASERECALIBRATOR#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_ESTIMATELIBRARYCOMPLEXITY.homo_sapiens - bam: Test Process GATK4_ESTIMATELIBRARYCOMPLEXITY#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_GENOTYPEGVCFS.homo_sapiens - [gvcf_gz, tbi, [], []], fasta, fai, dict, dbsnp, dbsnp_tbi: Test Process GATK4_GENOTYPEGVCFS#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_HAPLOTYPECALLER.homo_sapiens - [cram, crai] - fasta - fai - dict - sites - sites_tbi: Test Process GATK4_HAPLOTYPECALLER#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4SPARK_APPLYBQSR.sarscov2 - bam intervals: Test Process GATK4SPARK_APPLYBQSR#L1
Assertion failed: 2 of 2 assertions failed
Test Process GATK4SPARK_MARKDUPLICATES.homo_sapiens - bam - metrics: Test Process GATK4SPARK_MARKDUPLICATES#L1
Assertion failed: 6 of 6 assertions failed
Test Process LOFREQ_CALLPARALLEL.sarscov2 - bam: Test Process LOFREQ_CALLPARALLEL#L1
Assertion failed: 1 of 2 assertions failed
Test Process MOSDEPTH.homo_sapiens - cram, crai, []: Test Process MOSDEPTH#L1
Assertion failed: 1 of 2 assertions failed
Test Process NGSCHECKMATE_NCM.sarscov2 - vcf - stub: Test Process NGSCHECKMATE_NCM#L1
Assertion failed: 2 of 2 assertions failed
Test Process SENTIEON_BWAMEM.Paired-End: Test Process SENTIEON_BWAMEM#L1
Assertion failed: 2 of 2 assertions failed
Test Process SENTIEON_DEDUP.Test stub: Test Process SENTIEON_DEDUP#L1
Assertion failed: 2 of 2 assertions failed
Test Process SENTIEON_GVCFTYPER.sentieon gvcftyper dbsnp intervals: Test Process SENTIEON_GVCFTYPER#L1
Assertion failed: 2 of 2 assertions failed
Test Process SENTIEON_HAPLOTYPER.Sentieon Haplotyper Intervals BOTH: Test Process SENTIEON_HAPLOTYPER#L1
Assertion failed: 2 of 2 assertions failed
Test Process SNPEFF_DOWNLOAD.test-snpeff-download: Test Process SNPEFF_DOWNLOAD#L1
Assertion failed: 1 of 2 assertions failed
Test Process STRELKA_SOMATIC.human - cram - stub: Test Process STRELKA_SOMATIC#L1
Assertion failed: 1 of 2 assertions failed
Test Process TIDDIT_SV.sarscov2 - bam - stub: Test Process TIDDIT_SV#L1
Assertion failed: 1 of 2 assertions failed
Test Process BCFTOOLS_ANNOTATE.sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index: Test Process BCFTOOLS_ANNOTATE#L1
Assertion failed: 3 of 3 assertions failed
Test Process BCFTOOLS_ANNOTATE.sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index - stub: Test Process BCFTOOLS_ANNOTATE#L1
Assertion failed: 3 of 3 assertions failed
Test Process BCFTOOLS_MPILEUP.sarscov2 - [bam, []], fasta, true stub: Test Process BCFTOOLS_MPILEUP#L1
Assertion failed: 5 of 6 assertions failed
Test Process BCFTOOLS_SORT.sarscov2 - vcf_gz_index_csi: Test Process BCFTOOLS_SORT#L1
Assertion failed: 1 of 3 assertions failed
Test Process BCFTOOLS_SORT.sarscov2 - vcf_gz_index_tbi - stub: Test Process BCFTOOLS_SORT#L1
Assertion failed: 1 of 3 assertions failed
Test Process BWA_MEM.Paired-End: Test Process BWA_MEM#L1
Assertion failed: 1 of 2 assertions failed
Test Process BWAMEM2_INDEX.BWAMEM2 index: Test Process BWAMEM2_INDEX#L1
Assertion failed: 1 of 2 assertions failed
Test Process BWAMEM2_MEM.sarscov2 - [fastq1, fastq2], index, fasta, true - stub: Test Process BWAMEM2_MEM#L1
Assertion failed: 1 of 2 assertions failed
Test Process CNVKIT_BATCH.cnvkit batch wgs - bam: Test Process CNVKIT_BATCH#L1
Assertion failed: 1 of 2 assertions failed
Test Process CNVKIT_BATCH.cnvkit batch germline hybrid mode - bam: Test Process CNVKIT_BATCH#L1
Assertion failed: 1 of 2 assertions failed
Test Process CONTROLFREEC_ASSESSSIGNIFICANCE.human - freec_ratio: Test Process CONTROLFREEC_ASSESSSIGNIFICANCE#L1
Assertion failed: 1 of 3 assertions failed
Test Process DEEPVARIANT_RUNDEEPVARIANT.homo_sapiens - [bam, bai] - fasta - fai: Test Process DEEPVARIANT_RUNDEEPVARIANT#L1
Assertion failed: 1 of 2 assertions failed
Test Process DRAGMAP_ALIGN.sarscov2 - fastq, hashtable, fasta, true: Test Process DRAGMAP_ALIGN#L1
Assertion failed: 1 of 2 assertions failed
Test Process DRAGMAP_HASHTABLE.sarscov2 - fasta: Test Process DRAGMAP_HASHTABLE#L1
Assertion failed: 1 of 2 assertions failed
Test Process ENSEMBLVEP_VEP.test_ensemblvep_vep_fasta_tab_gz: Test Process ENSEMBLVEP_VEP#L1
Assertion failed: 2 of 3 assertions failed
Test Process FREEBAYES.sarscov2 - [ bam, bai, bam, bai ] - fasta - fai: Test Process FREEBAYES#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_BASERECALIBRATOR.sarscov2 - bam - multiple sites: Test Process GATK4_BASERECALIBRATOR#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_ESTIMATELIBRARYCOMPLEXITY.homo_sapiens - cram: Test Process GATK4_ESTIMATELIBRARYCOMPLEXITY#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_GENOMICSDBIMPORT.test_gatk4_genomicsdbimport_get_intervalslist: Test Process GATK4_GENOMICSDBIMPORT#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_GENOTYPEGVCFS.homo_sapiens - [gvcf_gz, tbi, bed, []], fasta, fai, dict, [], []: Test Process GATK4_GENOTYPEGVCFS#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_HAPLOTYPECALLER.homo_sapiens - [cram, crai, dragstr_model] - fasta - fai - dict - sites - sites_tbi: Test Process GATK4_HAPLOTYPECALLER#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4SPARK_APPLYBQSR.sarscov2 - bam - stub: Test Process GATK4SPARK_APPLYBQSR#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4SPARK_MARKDUPLICATES.homo_sapiens - cram: Test Process GATK4SPARK_MARKDUPLICATES#L1
Assertion failed: 2 of 2 assertions failed
Test Process LOFREQ_CALLPARALLEL.sarscov2 - bam - bed: Test Process LOFREQ_CALLPARALLEL#L1
Assertion failed: 1 of 2 assertions failed
Test Process MANTA_TUMORONLY.human - cram - bed: Test Process MANTA_TUMORONLY#L1
Assertion failed: 1 of 5 assertions failed
Test Process MOSDEPTH.homo_sapiens - cram, crai, bed: Test Process MOSDEPTH#L1
Assertion failed: 2 of 2 assertions failed
Test Process MOSDEPTH.homo_sapiens - bam, bai, [] - stub: Test Process MOSDEPTH#L1
Assertion failed: 1 of 2 assertions failed
Test Process SAMBLASTER.homo_sapiens-test_paired_end_umi_unsorted_bam: Test Process SAMBLASTER#L1
Assertion failed: 1 of 2 assertions failed
Test Process SAMTOOLS_MPILEUP.bam_bed: Test Process SAMTOOLS_MPILEUP#L1
Assertion failed: 2 of 3 assertions failed
Test Process SENTIEON_BWAMEM.Single-End - stub: Test Process SENTIEON_BWAMEM#L1
Assertion failed: 2 of 2 assertions failed
Test Process SENTIEON_GVCFTYPER.sentieon gvcftyper vcf: Test Process SENTIEON_GVCFTYPER#L1
Assertion failed: 2 of 2 assertions failed
Test Process SENTIEON_GVCFTYPER.sentieon gvcftyper - stub: Test Process SENTIEON_GVCFTYPER#L1
Assertion failed: 2 of 2 assertions failed
Test Process SENTIEON_HAPLOTYPER.Sentieon Haplotyper DBSNP BOTH: Test Process SENTIEON_HAPLOTYPER#L1
Assertion failed: 2 of 2 assertions failed
Test Process SNPEFF_DOWNLOAD.test-snpeff-download-stub: Test Process SNPEFF_DOWNLOAD#L1
Assertion failed: 1 of 2 assertions failed
Test Process TIDDIT_SV.sarscov2 - bam - bwa: Test Process TIDDIT_SV#L1
Assertion failed: 3 of 4 assertions failed
Test Process BCFTOOLS_ANNOTATE.sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_output: Test Process BCFTOOLS_ANNOTATE#L1
Assertion failed: 2 of 2 assertions failed
Test Process BCFTOOLS_ANNOTATE.sarscov2 - [vcf, [], annotation, annotation_tbi], header - bcf_output: Test Process BCFTOOLS_ANNOTATE#L1
Assertion failed: 2 of 2 assertions failed
Test Process BCFTOOLS_MPILEUP.sarscov2 - [bam, []], fasta, false stub: Test Process BCFTOOLS_MPILEUP#L1
Assertion failed: 4 of 5 assertions failed
Test Process BCFTOOLS_SORT.sarscov2 - vcf: Test Process BCFTOOLS_SORT#L1
Assertion failed: 1 of 2 assertions failed
Test Process BCFTOOLS_SORT.sarscov2 - vcf_gz_index - stub: Test Process BCFTOOLS_SORT#L1
Assertion failed: 1 of 3 assertions failed
Test Process BWA_MEM.Single-End: Test Process BWA_MEM#L1
Assertion failed: 1 of 2 assertions failed
Test Process BWAMEM2_MEM.sarscov2 - [fastq1, fastq2], index, fasta, false: Test Process BWAMEM2_MEM#L1
Assertion failed: 1 of 2 assertions failed
Test Process CNVKIT_ANTITARGET.human - bed - stub: Test Process CNVKIT_ANTITARGET#L1
Assertion failed: 1 of 2 assertions failed
Test Process CNVKIT_BATCH.cnvkit batch tumouronly mode - cram: Test Process CNVKIT_BATCH#L1
Assertion failed: 1 of 2 assertions failed
Test Process CNVKIT_REFERENCE.human - [fasta, bed]: Test Process CNVKIT_REFERENCE#L1
Assertion failed: 1 of 2 assertions failed
Test Process DEEPVARIANT_RUNDEEPVARIANT.homo_sapiens - [bam, bai] - fasta_gz - fasta_gz_fai: Test Process DEEPVARIANT_RUNDEEPVARIANT#L1
Assertion failed: 1 of 2 assertions failed
Test Process DRAGMAP_ALIGN.homo_sapiens - [fastq1, fastq2], hashtable, fasta, true: Test Process DRAGMAP_ALIGN#L1
Assertion failed: 1 of 2 assertions failed
Test Process ENSEMBLVEP_DOWNLOAD.celegans - download - stub: Test Process ENSEMBLVEP_DOWNLOAD#L1
Assertion failed: 1 of 2 assertions failed
Test Process FASTP.test_fastp_single_end_qc_only: Test Process FASTP#L1
Assertion failed: 1 of 4 assertions failed
Test Process FREEBAYES.sarscov2 - [ bam, bai, bed ] - fasta - fai: Test Process FREEBAYES#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_APPLYBQSR.sarscov2 - bam - intervals: Test Process GATK4_APPLYBQSR#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_BASERECALIBRATOR.sarscov2 - bam: Test Process GATK4_BASERECALIBRATOR#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_GENOTYPEGVCFS.homo_sapiens - [gvcf, idx, [], []], fasta, fai, dict, [], []: Test Process GATK4_GENOTYPEGVCFS#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4_HAPLOTYPECALLER.homo_sapiens - [cram, crai] - fasta - fai - dict: Test Process GATK4_HAPLOTYPECALLER#L1
Assertion failed: 1 of 2 assertions failed
Test Process GATK4SPARK_APPLYBQSR.sarscov2 - bam: Test Process GATK4SPARK_APPLYBQSR#L1
Assertion failed: 2 of 2 assertions failed
Test Process GATK4SPARK_MARKDUPLICATES.homo_sapiens - bam - multiple: Test Process GATK4SPARK_MARKDUPLICATES#L1
Assertion failed: 2 of 2 assertions failed
Test Process MOSDEPTH.homo_sapiens - bam, bai, bed: Test Process MOSDEPTH#L1
Assertion failed: 2 of 2 assertions failed
Test Process MOSDEPTH.homo_sapiens - bam, bai, bed - thresholds: Test Process MOSDEPTH#L1
Assertion failed: 2 of 2 assertions failed
Test Process NGSCHECKMATE_NCM.sarscov2 - bam - stub: Test Process NGSCHECKMATE_NCM#L1
Assertion failed: 2 of 2 assertions failed
Test Process SAMTOOLS_STATS.cram: Test Process SAMTOOLS_STATS#L1
Assertion failed: 1 of 2 assertions failed
Test Process SENTIEON_BWAMEM.Single-End Output CRAM: Test Process SENTIEON_BWAMEM#L1
Assertion failed: 2 of 2 assertions failed
Test Process SENTIEON_DEDUP.Test removing duplicates: Test Process SENTIEON_DEDUP#L1
Assertion failed: 2 of 2 assertions failed
Test Process SENTIEON_GVCFTYPER.sentieon gvcftyper intervals: Test Process SENTIEON_GVCFTYPER#L1
Assertion failed: 2 of 2 assertions failed
Test Process SENTIEON_HAPLOTYPER.Sentieon Haplotyper BOTH: Test Process SENTIEON_HAPLOTYPER#L1
Assertion failed: 2 of 2 assertions failed
Test Process SENTIEON_HAPLOTYPER.Sentieon Haplotyper - stub: Test Process SENTIEON_HAPLOTYPER#L1
Assertion failed: 2 of 2 assertions failed
Test Process SPRING_DECOMPRESS.Write-Two-Files: Test Process SPRING_DECOMPRESS#L1
Assertion failed: 2 of 2 assertions failed
Test Process TIDDIT_SV.human - cram - no_bwa: Test Process TIDDIT_SV#L1
Assertion failed: 3 of 4 assertions failed