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Update trimgalore module for save_unpaired fix #219

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Update trimgalore module for save_unpaired fix

Update trimgalore module for save_unpaired fix #219

Triggered via pull request January 6, 2025 16:34
@pinin4fjordspinin4fjords
synchronize #1482
Status Success
Total duration 41s
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template_version_comment.yml

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56 errors and 1 warning
Test Process TRIMGALORE.test_trimgalore_paired_end_keep_unpaired: Test Process TRIMGALORE#L1
Assertion failed: 2 of 2 assertions failed
Test Subworkflow FASTQ_FASTQC_UMITOOLS_TRIMGALORE.test single end read with UMI: Test Subworkflow FASTQ_FASTQC_UMITOOLS_TRIMGALORE#L1
Assertion failed: 1 of 3 assertions failed
Test Subworkflow FASTQ_FASTQC_UMITOOLS_TRIMGALORE.test paired end read with UMI: Test Subworkflow FASTQ_FASTQC_UMITOOLS_TRIMGALORE#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow FASTQ_FASTQC_UMITOOLS_TRIMGALORE.test paired end read without UMI: Test Subworkflow FASTQ_FASTQC_UMITOOLS_TRIMGALORE#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow FASTQ_FASTQC_UMITOOLS_TRIMGALORE.test single end read with UMI - stub: Test Subworkflow FASTQ_FASTQC_UMITOOLS_TRIMGALORE#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow FASTQ_FASTQC_UMITOOLS_TRIMGALORE.test paired end read with UMI - stub: Test Subworkflow FASTQ_FASTQC_UMITOOLS_TRIMGALORE#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow FASTQ_FASTQC_UMITOOLS_TRIMGALORE.test paired end read without UMI - stub: Test Subworkflow FASTQ_FASTQC_UMITOOLS_TRIMGALORE#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow FASTQ_FASTQC_UMITOOLS_TRIMGALORE.test single end read with UMI: Test Subworkflow FASTQ_FASTQC_UMITOOLS_TRIMGALORE#L1
Assertion failed: 1 of 3 assertions failed
Test Subworkflow FASTQ_FASTQC_UMITOOLS_TRIMGALORE.test paired end read with UMI: Test Subworkflow FASTQ_FASTQC_UMITOOLS_TRIMGALORE#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow FASTQ_FASTQC_UMITOOLS_TRIMGALORE.test paired end read without UMI: Test Subworkflow FASTQ_FASTQC_UMITOOLS_TRIMGALORE#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow FASTQ_FASTQC_UMITOOLS_TRIMGALORE.test single end read with UMI - stub: Test Subworkflow FASTQ_FASTQC_UMITOOLS_TRIMGALORE#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow FASTQ_FASTQC_UMITOOLS_TRIMGALORE.test paired end read with UMI - stub: Test Subworkflow FASTQ_FASTQC_UMITOOLS_TRIMGALORE#L1
Assertion failed: 1 of 2 assertions failed
Test Subworkflow FASTQ_FASTQC_UMITOOLS_TRIMGALORE.test paired end read without UMI - stub: Test Subworkflow FASTQ_FASTQC_UMITOOLS_TRIMGALORE#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 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 Process TRIMGALORE.test_trimgalore_paired_end_keep_unpaired: Test Process TRIMGALORE#L1
Assertion failed: 2 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 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 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 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 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 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 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 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 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 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 dummy UMI settings.Params: --aligner hisat2 --umi_dedup_tool 'umicollapse': Test pipeline with dummy UMI settings#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with dummy UMI settings.--umi_dedup_tool 'umitools': Test pipeline with dummy UMI settings#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with dummy UMI settings.--umi_dedup_tool 'umitools - stub: Test pipeline with dummy UMI settings#L1
Assertion failed: 1 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: 1 of 2 assertions failed
Test pipeline with dummy UMI settings.--umi_dedup_tool 'umitools': Test pipeline with dummy UMI settings#L1
Assertion failed: 1 of 2 assertions failed
Test pipeline with dummy UMI settings.--umi_dedup_tool 'umitools - stub: Test pipeline with dummy UMI 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 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
template_version
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636