bihealth / snappy-pipeline

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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

Build # 18878150394

Build Type

Pull #642

github

Committed by web-flow

Commit Message

Merge 80005e864 into 1e937d38c

Pull Request Pull Request #642: feat: migrate to snakemake v9

Run Details

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