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bihealth / snappy-pipeline
84%
master: 89%

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LAST BUILD BRANCH: snake9
DEFAULT BRANCH: master
Repo Added 25 Mar 2021 05:18PM UTC
Files 120
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LAST BUILD ON BRANCH snake9
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  • 102-110-fix-prepare-panel-parallel
  • 102-110-mutect2-mem-smk-profiles
  • 102-mutect2-wf-unittest
  • 102-parallel-wrapper-unittest
  • 105-bcftools-ci-issue
  • 113-variant-annotator-genome-release
  • 115-scatter-intervals-by-library-kit
  • 128-fix-copywriter-prepare-step-log
  • 130-bump-dependencies
  • 135-fix-freebayes-wrapper
  • 140-error-in-roh_calling-snakefile
  • 140-fix-roh-calling-workflow
  • 140-remove-roh-calling-workflow
  • 145-update-fastqc-wrapper-env
  • 148-bugs-in-ebfilter-wrapper
  • 155-expand-mutect2-parallel-tests
  • 156-somatic-end-to-end
  • 156-somatic-update
  • 157-update-delly
  • 163-fix-delly-single-sample
  • 164-ngs_mapping-crashes-for-target_cov_report
  • 166-fix-warnings-in-pytest-of-current-branch
  • 168-upgrade-varfish-annotator
  • 170-expose-rerun-triggers-of-new-snakemake-version
  • 172-add-310-to-ci
  • 176-fix-snappy-start-step
  • 182-update-java-vm-gc-option
  • 187-base-recalibration
  • 187-gatk4-base-recalibration
  • 188-make-delly-perform-per-family-calls-only
  • 196-add-optional-tag-default-config
  • 197-manta-is-stuck-when-executing-the-workflow
  • 200-snappy-packages-not-found-by-parallel-wrappers
  • 203-make-helper_gcnv_model-run-through-on-larger-projects
  • 205-bump-varfish-annotator-dependency
  • 206-compute-depth-of-coverage-track-for-wgs-in-ngs_mapping
  • 209-compute-b-allele-fraction-files-for-variant_calling
  • 210-arriba-in-somatic-gene-fusion-calling
  • 210-arriba-split-mapping-from-gene-fusion
  • 213-trimming-step
  • 218-adjust-gcnv-case-mode-to-perform-calls-per-family
  • 219-allow-merging-gcnv-output-from-different-kits
  • 220-target-seq-helper-gcnv-model
  • 223-gene-fusion-calling-broken
  • 224-refactor-gcnv-related-classes
  • 230-pin-mamba-version-ci
  • 233-bugs-in-panel-of-normals
  • 237-revive-cnvkit
  • 237-snakemake-job-log-files-misdirected
  • 239-change-default-depth-coverage-track
  • 241-fix-bug-target-seq-cnv-export
  • 245-snappys-varfish_annotator-swallows-manta-inversions
  • 249-tag-required-fields
  • 251-bump-varfish-annotator-version
  • 253-add-env-to-bcf-to-vcf-wrapper
  • 257-remove-erds-reference
  • 258-update-delly-file-name-wgs-sv-export
  • 260-fix-bug-vcf-sv-filter
  • 263-implement-long-read-pipeline-based-on-sniffles
  • 266-issues-in-cancer-end-to-end
  • 268-solve-n+1-issue-for-gcnv-based-calling
  • 269-change-rerun-triggers-to-snakemake-defaults
  • 270-enable-release-please
  • 472-adding-neoepitope-prediction-pipeline
  • 48-join-samples-by-custom-field
  • 49-validate-biosheet-v-config
  • 52-standardize-imports
  • 528-check-and-update-config-defaults
  • 54-unsupported-action
  • 573-revamp-somatic-sv-calling-purityploidy-estimation
  • 579-change-type-definition-for-ebfilter-model
  • 58-add-chunk-history-logic
  • 58-cnv-analysis-batch-mode
  • 58-integrate-batch-mode
  • 585-add-snakemake-parameter-to-snappy-pipeline
  • 587-preparation-for-somatic-cnv
  • 592_varfish_export_input_files
  • 599-sequenza-version-is-outdated
  • 6-fix-codacy-issues
  • 60-codacy-issues-targed-cnv-calling
  • 608-cbioportal_export-model-is-unclear-about-use-of-filtration
  • 620-class-genomename-in-model-cbioportal-export-incorrect
  • 622-conditional-target-coverage-report
  • 628-order-of-samples-inconsistent-in-mutect2-output
  • 65-fix-bwa-wrapper-encoding
  • 68-update-cubi-conda-url
  • 71-update-ruamel-yaml
  • 75-repeat-expansion
  • 77-mobile-element-insertion
  • 79-linkin-md5-rawdata-files
  • 83-cnv-analysis-cohort-case-mode
  • 84-pin-bcftools-version
  • 86-fix-xhmm-argument
  • add-simple-wrapper
  • bump/mehari
  • chore-update-mehari-0.36.3
  • coveralls
  • dependabot/pip/snakemake-gte-7.32.0-and-lt-10
  • dependabot/pip/snakemake-gte-7.32.0-and-lt-9
  • end_to_end_somatic
  • feat-various-smaller-issues
  • fix-ci-pytest
  • fix-ci-tests
  • fix-codacy-token-issues
  • fix-dependency-versions
  • fix-dryrun-tests
  • fix-formatting
  • fix-gcnv-model-expectations
  • fix-gcnv-params-for-targeted
  • fix-gcnv-wrapper-imports
  • fix-linting-in-ci
  • fix-manta-libboost
  • fix-mehari-wrapper
  • fix-peddy-call
  • fix-pydantic-version-in-tests
  • fix-resource-usage-input-functions
  • fix-wf-default-config-required
  • fix/644-somatic_ngs_fusion_calling
  • gcnv-with-background-samples
  • generalize-mutect2-wrapper
  • hotfix-manta-inversions
  • include-hgnc-tsv-in-mehari-params
  • join-pedigree-fix
  • main
  • master
  • move-config-access-to-params
  • mutect2_on_somatic_update
  • release-please--branches--main
  • remove-pytabix-dependency
  • remove-xhmm-config-dependency
  • restrict-pydantic-to-v2.9
  • scatter-gather
  • snake8
  • snake9
  • somatic-update
  • somatic_cnv_ascat
  • trimming_step_manual
  • trimming_step_more_unittests
  • update-biomedsheets-altamisa
  • update-cbioportal-export-model
  • update-cubi-conda-url
  • update-freebayes
  • update-ruff
  • varfish-annotator-external-data-sv-cnv
  • wgs-cnv-calling-add-delly
  • wgs-cnv-calling-add-gcnv
  • wgs-cnv-calling-remove-erds
  • wgs-sv-workflows

28 Oct 2025 02:26PM UTC coverage: 84.406% (+0.01%) from 84.394%
18878150394

Pull #642

github

web-flow
Merge 80005e864 into 1e937d38c
Pull Request #642: feat: migrate to snakemake v9

173 of 195 new or added lines in 47 files covered. (88.72%)

2 existing lines in 2 files now uncovered.

10030 of 11883 relevant lines covered (84.41%)

0.84 hits per line

Relevant lines Covered
Build:
Build:
11883 RELEVANT LINES 10030 COVERED LINES
0.84 HITS PER LINE
Source Files on master
  • Tree
  • List 120
  • Changed 15
  • Source Changed 0
  • Coverage Changed 15
Coverage ∆ File Lines Relevant Covered Missed Hits/Line

Recent builds

Builds Branch Commit Type Ran Committer Via Coverage
18878150394 snake9 Merge 80005e864 into 1e937d38c Pull #642 28 Oct 2025 02:32PM UTC web-flow github
84.41
18588052706 fix/644-somatic_ngs_fusion_calling Merge a7b44f5db into 1e937d38c Pull #645 17 Oct 2025 09:14AM UTC web-flow github
84.39
18192345688 snake9 Merge 1cb9a0b3a into 1e937d38c Pull #642 02 Oct 2025 12:08PM UTC web-flow github
84.4
18190988605 snake9 Merge 743285f14 into 1e937d38c Pull #642 02 Oct 2025 11:03AM UTC web-flow github
84.4
18160200325 snake8 Merge 8312b0c21 into 1e937d38c Pull #493 01 Oct 2025 11:13AM UTC web-flow github
84.4
18158442840 release-please--branches--main Merge 15eec7c0a into 1e937d38c Pull #641 01 Oct 2025 10:01AM UTC web-flow github
84.39
18158431154 main feat: move config accesses in wrappers to params (#536) Co-authored-by: Eric Blanc <eric.blanc@bihealth.de> push 01 Oct 2025 10:01AM UTC web-flow github
84.39
17868427401 move-config-access-to-params Merge 7acc5d731 into 1ecd7d784 Pull #536 19 Sep 2025 08:01PM UTC web-flow github pending completion  
17830093607 move-config-access-to-params Merge cc269e5a2 into 1ecd7d784 Pull #536 18 Sep 2025 01:28PM UTC web-flow github pending completion  
17765636567 main chore(main): release 0.4.0 (#581) push 16 Sep 2025 12:29PM UTC web-flow github
85.74
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