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Bump lots of modules so that conda versions have arm builds #46

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Bump lots of modules so that conda versions have arm builds

Bump lots of modules so that conda versions have arm builds #46

Triggered via pull request October 21, 2024 11:15
@pinin4fjordspinin4fjords
opened #1422
Status Success
Total duration 33s
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272 errors
Test Workflow BAM_MARKDUPLICATES_PICARD.sarscov2 - bam: Test Workflow BAM_MARKDUPLICATES_PICARD#L1
Assertion failed: 1 of 3 assertions failed
Test Workflow BAM_MARKDUPLICATES_PICARD.homo_sapiens - cram: Test Workflow BAM_MARKDUPLICATES_PICARD#L1
Assertion failed: 1 of 3 assertions failed
Test Workflow BAM_MARKDUPLICATES_PICARD.sarscov2 - bam - stub: Test Workflow BAM_MARKDUPLICATES_PICARD#L1
Assertion failed: 1 of 2 assertions failed
Test Workflow BAM_MARKDUPLICATES_PICARD.homo_sapiens - cram - stub: Test Workflow BAM_MARKDUPLICATES_PICARD#L1
Assertion failed: 1 of 2 assertions failed
Test Workflow QUANTIFY_RSEM.homo_sapiens - stub: Test Workflow QUANTIFY_RSEM#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow ALIGN_STAR.star - no igenomes: Test Subworkflow ALIGN_STAR#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow ALIGN_STAR.star - with igenomes: Test Subworkflow ALIGN_STAR#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow ALIGN_STAR.star - no igenomes - stub: Test Subworkflow ALIGN_STAR#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow ALIGN_STAR.star - with igenomes - stub: Test Subworkflow ALIGN_STAR#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
Assertion failed: 1 of 2 assertions failed
Test pipeline with Kallisto, skipping both QC and alignment.Params: --pseudo_aligner kallisto --skip_qc --skip_alignment - stub: Test pipeline with Kallisto, 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 HISAT2 aligner.Params: --aligner hisat2: Test pipeline with HISAT2 aligner#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with HISAT2 aligner.Params: --aligner hisat2 - stub: Test pipeline with HISAT2 aligner#L1
Assertion failed: 1 of 2 assertions failed
Test Workflow QUANTIFY_RSEM.homo_sapiens - stub: Test Workflow QUANTIFY_RSEM#L1
Assertion failed: 1 of 2 assertions failed
Test Workflow BAM_MARKDUPLICATES_PICARD.sarscov2 - bam: Test Workflow BAM_MARKDUPLICATES_PICARD#L1
Assertion failed: 1 of 3 assertions failed
Test Workflow BAM_MARKDUPLICATES_PICARD.homo_sapiens - cram: Test Workflow BAM_MARKDUPLICATES_PICARD#L1
Assertion failed: 1 of 3 assertions failed
Test Workflow BAM_MARKDUPLICATES_PICARD.sarscov2 - bam - stub: Test Workflow BAM_MARKDUPLICATES_PICARD#L1
Assertion failed: 1 of 2 assertions failed
Test Workflow BAM_MARKDUPLICATES_PICARD.homo_sapiens - cram - stub: Test Workflow BAM_MARKDUPLICATES_PICARD#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline by skipping trimming options.Params: --skip_trimming: Test pipeline by skipping trimming options#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with default settings.Params: default: Test pipeline with default settings#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with default settings.Params: default - stub: Test pipeline with default settings#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline by skipping QC options.Params: --skip_qc: Test pipeline by skipping QC options#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline by skipping QC options.Params: --skip_qc - stub: Test pipeline by skipping QC options#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow ALIGN_STAR.star - no igenomes: Test Subworkflow ALIGN_STAR#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow ALIGN_STAR.star - with igenomes: Test Subworkflow ALIGN_STAR#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow ALIGN_STAR.star - no igenomes - stub: Test Subworkflow ALIGN_STAR#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow ALIGN_STAR.star - with igenomes - stub: Test Subworkflow ALIGN_STAR#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline without a group type for featureCounts.Params: --featurecounts_group_type false: Test pipeline without a group type for featureCounts#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline without a group type for featureCounts.Params: --featurecounts_group_type false - stub: Test pipeline without a group type for featureCounts#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with a minimum mapped read threshold of 90.Params: --min_mapped_reads 90: Test pipeline with a minimum mapped read threshold of 90#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with a minimum mapped read threshold of 90.Params: --min_mapped_reads 90 - stub: Test pipeline with a minimum mapped read threshold of 90#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.default options: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gencode = false: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_gtf_filter: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_bbsplit: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_alignment: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_pseudo_alignment: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gtf = false: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gff = false: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gfp = false: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.transcriptome = false: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.with bed: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.rsem_index = false: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.salmon_index = false: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.hisat2_index = false: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gencode = true: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.featurecounts_group_type = 'gene_type': Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_gtf_filter = true: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_bbsplit = true: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_alignment = true: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_pseudoalignment = true: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.default options - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gencode = false - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_gtf_filter - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_bbsplit - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_alignment - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_pseudo_alignment - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gtf = false - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gff = false - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gfp = false - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.transcriptome = false - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.with bed - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.rsem_index = false - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.salmon_index = false - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.hisat2_index = false - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gencode = true - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.featurecounts_group_type = 'gene_type' - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_gtf_filter = true - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_bbsplit = true - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_alignment = true - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_pseudoalignment = true - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with STAR aligner and RSEM for quantification.Params: --aligner star_rsem: Test pipeline with STAR aligner and RSEM for quantification#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with STAR aligner and RSEM for quantification.Params: --aligner star_rsem - stub: Test pipeline with STAR aligner and RSEM for quantification#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
Assertion failed: 1 of 2 assertions failed
Test pipeline with Kallisto, skipping both QC and alignment.Params: --pseudo_aligner kallisto --skip_qc --skip_alignment - stub: Test pipeline with Kallisto, skipping both QC and alignment#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with ribosomal RNA removal.Params: --remove_ribo_rna: Test pipeline with ribosomal RNA removal#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with ribosomal RNA removal.Params: --remove_ribo_rna - stub: Test pipeline with ribosomal RNA removal#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline by skipping QC options.Params: --skip_qc: Test pipeline by skipping QC options#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline by skipping QC options.Params: --skip_qc - stub: Test pipeline by skipping QC options#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.default options: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gencode = false: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_gtf_filter: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_bbsplit: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_alignment: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_pseudo_alignment: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gtf = false: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gff = false: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gfp = false: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.transcriptome = false: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.with bed: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.rsem_index = false: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.salmon_index = false: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.hisat2_index = false: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gencode = true: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.featurecounts_group_type = 'gene_type': Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_gtf_filter = true: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_bbsplit = true: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_alignment = true: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_pseudoalignment = true: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.default options - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gencode = false - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_gtf_filter - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_bbsplit - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_alignment - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_pseudo_alignment - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gtf = false - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gff = false - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gfp = false - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.transcriptome = false - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.with bed - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.rsem_index = false - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.salmon_index = false - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.hisat2_index = false - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gencode = true - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.featurecounts_group_type = 'gene_type' - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_gtf_filter = true - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_bbsplit = true - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_alignment = true - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_pseudoalignment = true - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline by skipping trimming options.Params: --skip_trimming: Test pipeline by skipping trimming options#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with HISAT2 aligner.Params: --aligner hisat2: Test pipeline with HISAT2 aligner#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with HISAT2 aligner.Params: --aligner hisat2 - stub: Test pipeline with HISAT2 aligner#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with a minimum mapped read threshold of 90.Params: --min_mapped_reads 90: Test pipeline with a minimum mapped read threshold of 90#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with a minimum mapped read threshold of 90.Params: --min_mapped_reads 90 - stub: Test pipeline with a minimum mapped read threshold of 90#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline without a group type for featureCounts.Params: --featurecounts_group_type false: Test pipeline without a group type for featureCounts#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline without a group type for featureCounts.Params: --featurecounts_group_type false - stub: Test pipeline without a group type for featureCounts#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with STAR aligner and RSEM for quantification.Params: --aligner star_rsem: Test pipeline with STAR aligner and RSEM for quantification#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with STAR aligner and RSEM for quantification.Params: --aligner star_rsem - stub: Test pipeline with STAR aligner and RSEM for quantification#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with default settings.Params: default: Test pipeline with default settings#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with default settings.Params: default - stub: Test pipeline with default settings#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with ribosomal RNA removal.Params: --remove_ribo_rna: Test pipeline with ribosomal RNA removal#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with ribosomal RNA removal.Params: --remove_ribo_rna - stub: Test pipeline with ribosomal RNA removal#L1
Assertion failed: 1 of 2 assertions failed
Test Workflow BAM_MARKDUPLICATES_PICARD.sarscov2 - bam: Test Workflow BAM_MARKDUPLICATES_PICARD#L1
Assertion failed: 1 of 3 assertions failed
Test Workflow BAM_MARKDUPLICATES_PICARD.homo_sapiens - cram: Test Workflow BAM_MARKDUPLICATES_PICARD#L1
Assertion failed: 1 of 3 assertions failed
Test Workflow BAM_MARKDUPLICATES_PICARD.sarscov2 - bam - stub: Test Workflow BAM_MARKDUPLICATES_PICARD#L1
Assertion failed: 1 of 2 assertions failed
Test Workflow BAM_MARKDUPLICATES_PICARD.homo_sapiens - cram - stub: Test Workflow BAM_MARKDUPLICATES_PICARD#L1
Assertion failed: 1 of 2 assertions failed
Test Workflow QUANTIFY_RSEM.homo_sapiens - stub: Test Workflow QUANTIFY_RSEM#L1
Assertion failed: 1 of 2 assertions failed
Test Workflow QUANTIFY_RSEM.homo_sapiens - stub: Test Workflow QUANTIFY_RSEM#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow ALIGN_STAR.star - no igenomes: Test Subworkflow ALIGN_STAR#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow ALIGN_STAR.star - with igenomes: Test Subworkflow ALIGN_STAR#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow ALIGN_STAR.star - no igenomes - stub: Test Subworkflow ALIGN_STAR#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow ALIGN_STAR.star - with igenomes - stub: Test Subworkflow ALIGN_STAR#L1
Assertion failed: 1 of 2 assertions failed
Test Workflow BAM_MARKDUPLICATES_PICARD.sarscov2 - bam: Test Workflow BAM_MARKDUPLICATES_PICARD#L1
Assertion failed: 1 of 3 assertions failed
Test Workflow BAM_MARKDUPLICATES_PICARD.homo_sapiens - cram: Test Workflow BAM_MARKDUPLICATES_PICARD#L1
Assertion failed: 1 of 3 assertions failed
Test Workflow BAM_MARKDUPLICATES_PICARD.sarscov2 - bam - stub: Test Workflow BAM_MARKDUPLICATES_PICARD#L1
Assertion failed: 1 of 2 assertions failed
Test Workflow BAM_MARKDUPLICATES_PICARD.homo_sapiens - cram - stub: Test Workflow BAM_MARKDUPLICATES_PICARD#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
Assertion failed: 1 of 2 assertions failed
Test pipeline with Kallisto, skipping both QC and alignment.Params: --pseudo_aligner kallisto --skip_qc --skip_alignment - stub: Test pipeline with Kallisto, 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 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
Assertion failed: 1 of 2 assertions failed
Test pipeline with Kallisto, skipping both QC and alignment.Params: --pseudo_aligner kallisto --skip_qc --skip_alignment - stub: Test pipeline with Kallisto, skipping both QC and alignment#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline by skipping QC options.Params: --skip_qc: Test pipeline by skipping QC options#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline by skipping QC options.Params: --skip_qc - stub: Test pipeline by skipping QC options#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline by skipping QC options.Params: --skip_qc: Test pipeline by skipping QC options#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline by skipping QC options.Params: --skip_qc - stub: Test pipeline by skipping QC options#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with HISAT2 aligner.Params: --aligner hisat2: Test pipeline with HISAT2 aligner#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with HISAT2 aligner.Params: --aligner hisat2 - stub: Test pipeline with HISAT2 aligner#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with HISAT2 aligner.Params: --aligner hisat2: Test pipeline with HISAT2 aligner#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with HISAT2 aligner.Params: --aligner hisat2 - stub: Test pipeline with HISAT2 aligner#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline by skipping trimming options.Params: --skip_trimming: Test pipeline by skipping trimming options#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with STAR aligner and RSEM for quantification.Params: --aligner star_rsem: Test pipeline with STAR aligner and RSEM for quantification#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with STAR aligner and RSEM for quantification.Params: --aligner star_rsem - stub: Test pipeline with STAR aligner and RSEM for quantification#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow ALIGN_STAR.star - no igenomes: Test Subworkflow ALIGN_STAR#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow ALIGN_STAR.star - with igenomes: Test Subworkflow ALIGN_STAR#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow ALIGN_STAR.star - no igenomes - stub: Test Subworkflow ALIGN_STAR#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow ALIGN_STAR.star - with igenomes - stub: Test Subworkflow ALIGN_STAR#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline without a group type for featureCounts.Params: --featurecounts_group_type false: Test pipeline without a group type for featureCounts#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline without a group type for featureCounts.Params: --featurecounts_group_type false - stub: Test pipeline without a group type for featureCounts#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with a minimum mapped read threshold of 90.Params: --min_mapped_reads 90: Test pipeline with a minimum mapped read threshold of 90#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with a minimum mapped read threshold of 90.Params: --min_mapped_reads 90 - stub: Test pipeline with a minimum mapped read threshold of 90#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with STAR aligner and RSEM for quantification.Params: --aligner star_rsem: Test pipeline with STAR aligner and RSEM for quantification#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with STAR aligner and RSEM for quantification.Params: --aligner star_rsem - stub: Test pipeline with STAR aligner and RSEM for quantification#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with default settings.Params: default: Test pipeline with default settings#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with default settings.Params: default - stub: Test pipeline with default settings#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline without a group type for featureCounts.Params: --featurecounts_group_type false: Test pipeline without a group type for featureCounts#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline without a group type for featureCounts.Params: --featurecounts_group_type false - stub: Test pipeline without a group type for featureCounts#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with default settings.Params: default: Test pipeline with default settings#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with default settings.Params: default - stub: Test pipeline with default settings#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.default options: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gencode = false: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_gtf_filter: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_bbsplit: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_alignment: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_pseudo_alignment: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gtf = false: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gff = false: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gfp = false: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.transcriptome = false: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.with bed: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.rsem_index = false: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.salmon_index = false: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.hisat2_index = false: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gencode = true: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.featurecounts_group_type = 'gene_type': Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_gtf_filter = true: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_bbsplit = true: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_alignment = true: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_pseudoalignment = true: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.default options - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gencode = false - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_gtf_filter - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_bbsplit - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_alignment - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_pseudo_alignment - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gtf = false - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gff = false - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gfp = false - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.transcriptome = false - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.with bed - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.rsem_index = false - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.salmon_index = false - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.hisat2_index = false - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gencode = true - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.featurecounts_group_type = 'gene_type' - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_gtf_filter = true - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_bbsplit = true - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_alignment = true - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_pseudoalignment = true - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with a minimum mapped read threshold of 90.Params: --min_mapped_reads 90: Test pipeline with a minimum mapped read threshold of 90#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with a minimum mapped read threshold of 90.Params: --min_mapped_reads 90 - stub: Test pipeline with a minimum mapped read threshold of 90#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.default options: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gencode = false: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_gtf_filter: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_bbsplit: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_alignment: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_pseudo_alignment: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gtf = false: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gff = false: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gfp = false: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.transcriptome = false: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.with bed: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.rsem_index = false: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.salmon_index = false: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.hisat2_index = false: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gencode = true: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.featurecounts_group_type = 'gene_type': Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_gtf_filter = true: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_bbsplit = true: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_alignment = true: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_pseudoalignment = true: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.default options - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gencode = false - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_gtf_filter - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_bbsplit - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_alignment - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_pseudo_alignment - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gtf = false - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gff = false - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gfp = false - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.transcriptome = false - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.with bed - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.rsem_index = false - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.salmon_index = false - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.hisat2_index = false - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gencode = true - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.featurecounts_group_type = 'gene_type' - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_gtf_filter = true - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_bbsplit = true - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_alignment = true - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_pseudoalignment = true - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline by skipping trimming options.Params: --skip_trimming: Test pipeline by skipping trimming options#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with ribosomal RNA removal.Params: --remove_ribo_rna: Test pipeline with ribosomal RNA removal#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with ribosomal RNA removal.Params: --remove_ribo_rna - stub: Test pipeline with ribosomal RNA removal#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with ribosomal RNA removal.Params: --remove_ribo_rna: Test pipeline with ribosomal RNA removal#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with ribosomal RNA removal.Params: --remove_ribo_rna - stub: Test pipeline with ribosomal RNA removal#L1
Assertion failed: 1 of 2 assertions failed