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Make genomic FASTA input optional #235

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Make genomic FASTA input optional

Make genomic FASTA input optional #235

Triggered via pull request January 21, 2025 19:02
@pinin4fjordspinin4fjords
synchronize #1490
Status Success
Total duration 36s
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83 errors and 1 warning
Test Process SALMON_INDEX.sarscov2: Test Process SALMON_INDEX#L1
Assertion failed: 3 of 3 assertions failed
Test Process SALMON_INDEX.sarscov2 transcriptome only: Test Process SALMON_INDEX#L1
Assertion failed: 3 of 3 assertions failed
Test Process SALMON_INDEX.sarscov2 stub: Test Process SALMON_INDEX#L1
Assertion failed: 3 of 3 assertions failed
Test pipeline by skipping trimming options.Params: --skip_trimming: Test pipeline by skipping trimming options#L1
Assertion failed: 2 of 2 assertions failed
Test Workflow FASTQ_SUBSAMPLE_FQ_SALMON.homo_sapiens paired-end [fastq]: Test Workflow FASTQ_SUBSAMPLE_FQ_SALMON#L1
java.lang.NullPointerException: Cannot invoke method getAt() on null object
Test Workflow FASTQ_SUBSAMPLE_FQ_SALMON.homo_sapiens paired-end [fastq] - stub: Test Workflow FASTQ_SUBSAMPLE_FQ_SALMON#L1
java.lang.NullPointerException: Cannot invoke method getAt() on null object
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: 2 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: 2 of 2 assertions failed
Test pipeline by omitting fasta input.Params: no fasta: Test pipeline by omitting fasta input#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline with ribosomal RNA removal.Params: --remove_ribo_rna: Test pipeline with ribosomal RNA removal#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline with ribosomal RNA removal.Params: --remove_ribo_rna - stub: Test pipeline with ribosomal RNA removal#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline with HISAT2 aligner.Params: --aligner hisat2: Test pipeline with HISAT2 aligner#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline with HISAT2 aligner.Params: --aligner hisat2 - stub: Test pipeline with HISAT2 aligner#L1
Assertion failed: 2 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: 2 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: 2 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: 2 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: 2 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: 2 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: 2 of 2 assertions failed
Test Process GTF_FILTER.sarscov2 - fasta - gtf: Test Process GTF_FILTER#L1
Assertion failed: 2 of 2 assertions failed
Test Process GTF_FILTER.sarscov2 - fasta - gtf - stub: Test Process GTF_FILTER#L1
Assertion failed: 2 of 2 assertions failed
Test Workflow QUANTIFY_PSEUDO_ALIGNMENT.salmon: Test Workflow QUANTIFY_PSEUDO_ALIGNMENT#L1
Assertion failed: 2 of 2 assertions failed
Test Workflow QUANTIFY_PSEUDO_ALIGNMENT.kallisto: Test Workflow QUANTIFY_PSEUDO_ALIGNMENT#L1
Assertion failed: 2 of 2 assertions failed
Test Workflow QUANTIFY_PSEUDO_ALIGNMENT.salmon - stub: Test Workflow QUANTIFY_PSEUDO_ALIGNMENT#L1
Assertion failed: 2 of 2 assertions failed
Test Workflow QUANTIFY_PSEUDO_ALIGNMENT.kallisto - stub: Test Workflow QUANTIFY_PSEUDO_ALIGNMENT#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline by skipping QC options.Params: --skip_qc: Test pipeline by skipping QC options#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline by skipping QC options.Params: --skip_qc - stub: Test pipeline by skipping QC options#L1
Assertion failed: 2 of 2 assertions failed
Test Process SALMON_QUANT.sarscov2 - single_end: Test Process SALMON_QUANT#L1
Assertion failed: 4 of 4 assertions failed
Test Process SALMON_QUANT.sarscov2 - single_end stub: Test Process SALMON_QUANT#L1
Assertion failed: 4 of 4 assertions failed
Test Process SALMON_QUANT.sarscov2 - single_end lib type A: Test Process SALMON_QUANT#L1
Assertion failed: 4 of 4 assertions failed
Test Process SALMON_QUANT.sarscov2 - single_end lib type A stub: Test Process SALMON_QUANT#L1
Assertion failed: 4 of 4 assertions failed
Test Process SALMON_QUANT.sarscov2 - pair_end: Test Process SALMON_QUANT#L1
Assertion failed: 4 of 4 assertions failed
Test Process SALMON_QUANT.sarscov2 - pair_end stub: Test Process SALMON_QUANT#L1
Assertion failed: 4 of 4 assertions failed
Test Process SALMON_QUANT.sarscov2 - pair_end multiple: Test Process SALMON_QUANT#L1
Assertion failed: 4 of 4 assertions failed
Test Process SALMON_QUANT.sarscov2 - pair_end multiple stub: Test Process SALMON_QUANT#L1
Assertion failed: 4 of 4 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: 2 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: 2 of 2 assertions failed
Test pipeline with dummy UMI settings.Params: --aligner hisat2 --umi_dedup_tool 'umicollapse': Test pipeline with dummy UMI settings#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline with dummy UMI settings.--umi_dedup_tool 'umitools': Test pipeline with dummy UMI settings#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline with dummy UMI settings.--umi_dedup_tool 'umitools - stub: Test pipeline with dummy UMI settings#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline with default settings.Params: default: Test pipeline with default settings#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline with default settings.Params: default - stub: Test pipeline with default settings#L1
Assertion failed: 2 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.default options: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 2 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gencode = false: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 2 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_gtf_filter: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 2 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_bbsplit: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 2 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_alignment: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 2 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_pseudo_alignment: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 2 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gtf = false: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 2 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gff = false: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 2 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gfp = false: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 2 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.transcriptome = false: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 2 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.with bed: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 2 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.rsem_index = false: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 2 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.salmon_index = false: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 2 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.hisat2_index = false: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 2 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gencode = true: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 2 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.featurecounts_group_type = 'gene_type': Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 2 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_gtf_filter = true: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 2 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_bbsplit = true: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 2 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_alignment = true: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 2 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_pseudoalignment = true: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 2 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.default options - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 2 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gencode = false - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 2 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_gtf_filter - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 2 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_bbsplit - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 2 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_alignment - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 2 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_pseudo_alignment - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 2 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gtf = false - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 2 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gff = false - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 2 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gfp = false - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 2 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.transcriptome = false - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 2 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.with bed - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 2 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.rsem_index = false - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 2 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.salmon_index = false - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 2 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.hisat2_index = false - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 2 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gencode = true - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 2 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.featurecounts_group_type = 'gene_type' - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 2 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_gtf_filter = true - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 2 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_bbsplit = true - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 2 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_alignment = true - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 2 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.skip_pseudoalignment = true - stub: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 2 of 2 assertions failed
Test Subworkflow PREPARE_GENOME.gfp = false: Test Subworkflow PREPARE_GENOME#L1
Assertion failed: 1 of 2 assertions failed
template_version
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636