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feat: release 9.0.0#902

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ashwini06 merged 71 commits intomasterClinical-Genomics/BALSAMIC:masterfrom release/9_0_0Clinical-Genomics/BALSAMIC:release/9_0_0Copy head branch name to clipboardMay 3, 2022

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Commits

Commits on Dec 13, 2021

• add interval bed option to umi TNscope

  

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• add tests

  

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• update changelog

  

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• fix black

  

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• update padding to 100

  

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Commits on Dec 17, 2021

• Merge pull request #837 from Clinical-Genomics/fix/umi_intervalbed

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Commits on Dec 20, 2021

• Merge branch 'master' into develop

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Commits on Dec 22, 2021

• feat: generate canfam3 references (#843)

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Commits on Dec 23, 2021

• refactor: merge QC metric extraction workflows (#833)

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Commits on Jan 4, 2022

• add umi dups metrics to multiqc

  

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• remove wrong spacing for comments

  

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• add changelog

  

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Commits on Jan 11, 2022

• remove fastp exclusion

  

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• update changelog

  

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Commits on Jan 13, 2022

• #845 from Clinical-Genomics/feat/umi_duprate

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Commits on Jan 24, 2022

• fix: capture kit empty argument for WGS runs (#850)

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Commits on Feb 7, 2022

• fix: QC panel bed version generalisation (#855)

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Commits on Feb 9, 2022

• Merge branch 'master' into develop

  

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Commits on Feb 16, 2022

• merge master changes to develop

  

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Commits on Feb 24, 2022

• add vcf2cytosure container

  

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• add vcf2cytosure container tests

  

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• update changelog

  

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• add newlines

  

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Commits on Feb 28, 2022

• add vcf2cytosure to git actions

  

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• change alpine version

  

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• remove previous pip install vcf2cytosure

  

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• fix label key in dockerfile

  

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• test balsamic container image to updated version

  

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Commits on Mar 1, 2022

• remove vcf2cytosure from annotate tests

  

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• test invalide label key

  

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• test invalide label key

  

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  2fed80c

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• fix invalid label key

  

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• remove --no-cache-dir from pip dockerfile

  

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Commits on Mar 2, 2022

• update changelog

  

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• add vcf2cytosure to commons

  

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  5c3d5b5

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• fix black linter

  

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Commits on Mar 3, 2022

• feat: add SVDB (#872)

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Commits on Mar 4, 2022

• fix pythonpath

  

  ashwini06

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• fix conflicts

  

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Commits on Mar 7, 2022

• Merge pull request #869 from Clinical-Genomics/feat/add_vcf2cytosure

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Commits on Mar 8, 2022

• feat: add svdb workflow (#873)

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Commits on Mar 9, 2022

• feat: add svdb workflow tga (#879)

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• merge changes from master

  

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Commits on Mar 14, 2022

• feat: create cgh files from cnvkit outputs (#880)

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Commits on Mar 15, 2022

• feat: svdb merge sv cnv (#886)

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Commits on Mar 16, 2022

• feat: remove sv and cnv callers from annotation and filter rules (#889)

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Commits on Mar 28, 2022

• feat: remove vcfanno and cosmic for sv (#891)

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Commits on Apr 4, 2022

• fix: update svdb to 2.6.0 (#901)

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• feat: Option to use PON with TGA cnvkit (#851)

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  ivadym

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• merge master changes to develop

  

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• update changelog

  

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Commits on Apr 6, 2022

• refactor: redundant files and varaibles from balsamic (#903)

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• update changelog and correct it

  

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Commits on Apr 11, 2022

• feat: extract additional WGS QC metrics (#907)

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Commits on Apr 12, 2022

• merge master changes to develop

  

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Commits on Apr 13, 2022

• fix: remove stat files and add count files for scout upload VCFs (#899)

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Commits on Apr 19, 2022

• docs: balsamic methods description in readthedocs (#906)

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• feat: add ascatngs copynumber (#914)

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• refactor: remove QC delivery report wokflow (#913)

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• Merge branch 'develop' into release/9_0_0

  

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Commits on Apr 20, 2022

• feat: add qc only workflow (#847)

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• docs: add annotation resources (#916)

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Commits on Apr 22, 2022

• feat: update delly (#920)

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Commits on Apr 26, 2022

• fix: Change of gnomad pop freq value for UMI workflow (#919)

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Commits on Apr 27, 2022

• feat: add Delly CNV for tumor only workflow (#923)

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Commits on Apr 28, 2022

• feat: add delly CNV read-depth profile (#924)

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Commits on Apr 29, 2022

• refactor: Remove gatk haplotypcaller (#922)

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Commits on May 2, 2022

• refactor: balsamic containers (#921)

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• refactor: Update the list of files to be stored and delivered (#915)

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• feat: bcftools counts QC validation (#925)

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• Merge branch 'develop' into release/9_0_0

  

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