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Add umicollapse as an alternative to umi-tools #3179

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Add umicollapse as an alternative to umi-tools

Add umicollapse as an alternative to umi-tools #3179

Re-run triggered December 4, 2024 13:10
@pinin4fjordspinin4fjords
#1369
siddharthab:umicollapse
Status Success
Total duration 29m 40s
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ci.yml

on: pull_request
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Matrix: test
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34 errors and 70 warnings
Run tests (subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/tests/main.nf.test docker NF-latest-everything)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_initialisation.workflow.nf.test docker NF-24.04.2)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_initialisation.workflow.nf.test docker NF-latest-everything)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test docker NF-24.04.2)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_completion.workflow.nf.test docker NF-latest-everything)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/tests/main.nf.test docker NF-24.04.2)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (modules/nf-core/umicollapse/tests/main.nf.test docker NF-24.04.2)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test docker NF-latest-everything)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (modules/nf-core/umicollapse/tests/main.nf.test docker NF-latest-everything)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (modules/nf-core/umitools/dedup/tests/main.nf.test docker NF-latest-everything)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.function.nf.test docker NF-latest-everything)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (tests/salmon.nf.test docker NF-latest-everything)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.function.nf.test docker NF-24.04.2)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (tests/kallisto.nf.test docker NF-latest-everything)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (modules/nf-core/umitools/dedup/tests/main.nf.test docker NF-24.04.2)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (tests/kallisto.nf.test docker NF-24.04.2)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (tests/salmon.nf.test docker NF-24.04.2)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (tests/skip_qc.nf.test docker NF-latest-everything)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (tests/skip_trimming.nf.test docker NF-latest-everything)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (tests/hisat2.nf.test docker NF-latest-everything)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_completion.workflow.nf.test docker NF-24.04.2)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (tests/featurecounts_group_type.nf.test docker NF-latest-everything)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (tests/skip_trimming.nf.test docker NF-24.04.2)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (tests/hisat2.nf.test docker NF-24.04.2)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (tests/star_rsem.nf.test docker NF-latest-everything)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (tests/min_mapped_reads.nf.test docker NF-24.04.2)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (tests/featurecounts_group_type.nf.test docker NF-24.04.2)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (tests/default.nf.test docker NF-latest-everything)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (tests/star_rsem.nf.test docker NF-24.04.2)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (tests/min_mapped_reads.nf.test docker NF-latest-everything)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (tests/remove_ribo_rna.nf.test docker NF-24.04.2)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (tests/default.nf.test docker NF-24.04.2)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (tests/skip_qc.nf.test docker NF-24.04.2)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Run tests (tests/remove_ribo_rna.nf.test docker NF-latest-everything)
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Check for changes
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
Run tests (subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/tests/main.nf.test docker NF-latest-everything)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
Run tests (subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/tests/main.nf.test docker NF-latest-everything)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Run tests (subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_initialisation.workflow.nf.test docker NF-24.04.2)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
Run tests (subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_initialisation.workflow.nf.test docker NF-24.04.2)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Run tests (subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_initialisation.workflow.nf.test docker NF-latest-everything)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
Run tests (subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_initialisation.workflow.nf.test docker NF-latest-everything)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Run tests (subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test docker NF-24.04.2)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
Run tests (subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test docker NF-24.04.2)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Run tests (subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_completion.workflow.nf.test docker NF-latest-everything)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
Run tests (subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_completion.workflow.nf.test docker NF-latest-everything)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Run tests (subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/tests/main.nf.test docker NF-24.04.2)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
Run tests (subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/tests/main.nf.test docker NF-24.04.2)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Run tests (modules/nf-core/umicollapse/tests/main.nf.test docker NF-24.04.2)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
Run tests (modules/nf-core/umicollapse/tests/main.nf.test docker NF-24.04.2)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Run tests (subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test docker NF-latest-everything)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
Run tests (subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test docker NF-latest-everything)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Run tests (modules/nf-core/umicollapse/tests/main.nf.test docker NF-latest-everything)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
Run tests (modules/nf-core/umicollapse/tests/main.nf.test docker NF-latest-everything)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Run tests (modules/nf-core/umitools/dedup/tests/main.nf.test docker NF-latest-everything)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
Run tests (modules/nf-core/umitools/dedup/tests/main.nf.test docker NF-latest-everything)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Run tests (subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.function.nf.test docker NF-latest-everything)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
Run tests (subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.function.nf.test docker NF-latest-everything)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Run tests (tests/salmon.nf.test docker NF-latest-everything)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
Run tests (tests/salmon.nf.test docker NF-latest-everything)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Run tests (subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.function.nf.test docker NF-24.04.2)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
Run tests (subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.function.nf.test docker NF-24.04.2)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Run tests (tests/kallisto.nf.test docker NF-latest-everything)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
Run tests (tests/kallisto.nf.test docker NF-latest-everything)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Run tests (modules/nf-core/umitools/dedup/tests/main.nf.test docker NF-24.04.2)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
Run tests (modules/nf-core/umitools/dedup/tests/main.nf.test docker NF-24.04.2)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Run tests (tests/kallisto.nf.test docker NF-24.04.2)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
Run tests (tests/kallisto.nf.test docker NF-24.04.2)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Run tests (tests/salmon.nf.test docker NF-24.04.2)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
Run tests (tests/salmon.nf.test docker NF-24.04.2)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Run tests (tests/skip_qc.nf.test docker NF-latest-everything)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
Run tests (tests/skip_qc.nf.test docker NF-latest-everything)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Run tests (tests/skip_trimming.nf.test docker NF-latest-everything)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
Run tests (tests/skip_trimming.nf.test docker NF-latest-everything)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Run tests (tests/hisat2.nf.test docker NF-latest-everything)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
Run tests (tests/hisat2.nf.test docker NF-latest-everything)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Run tests (subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_completion.workflow.nf.test docker NF-24.04.2)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
Run tests (subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_completion.workflow.nf.test docker NF-24.04.2)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Run tests (tests/featurecounts_group_type.nf.test docker NF-latest-everything)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
Run tests (tests/featurecounts_group_type.nf.test docker NF-latest-everything)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Run tests (tests/skip_trimming.nf.test docker NF-24.04.2)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
Run tests (tests/skip_trimming.nf.test docker NF-24.04.2)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Run tests (tests/hisat2.nf.test docker NF-24.04.2)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
Run tests (tests/hisat2.nf.test docker NF-24.04.2)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Run tests (tests/star_rsem.nf.test docker NF-latest-everything)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
Run tests (tests/star_rsem.nf.test docker NF-latest-everything)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Run tests (tests/min_mapped_reads.nf.test docker NF-24.04.2)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
Run tests (tests/min_mapped_reads.nf.test docker NF-24.04.2)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Run tests (tests/featurecounts_group_type.nf.test docker NF-24.04.2)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
Run tests (tests/featurecounts_group_type.nf.test docker NF-24.04.2)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Run tests (tests/default.nf.test docker NF-latest-everything)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
Run tests (tests/default.nf.test docker NF-latest-everything)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Run tests (tests/star_rsem.nf.test docker NF-24.04.2)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
Run tests (tests/star_rsem.nf.test docker NF-24.04.2)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Run tests (tests/min_mapped_reads.nf.test docker NF-latest-everything)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
Run tests (tests/min_mapped_reads.nf.test docker NF-latest-everything)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Run tests (tests/remove_ribo_rna.nf.test docker NF-24.04.2)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
Run tests (tests/remove_ribo_rna.nf.test docker NF-24.04.2)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Run tests (tests/default.nf.test docker NF-24.04.2)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
Run tests (tests/default.nf.test docker NF-24.04.2)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Run tests (tests/skip_qc.nf.test docker NF-24.04.2)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
Run tests (tests/skip_qc.nf.test docker NF-24.04.2)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Run tests (tests/remove_ribo_rna.nf.test docker NF-latest-everything)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
Run tests (tests/remove_ribo_rna.nf.test docker NF-latest-everything)
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
confirm-pass
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636