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Release/8 0 0#674

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hassanfa merged 68 commits intomasterClinical-Genomics/BALSAMIC:masterfrom release/8_0_0Clinical-Genomics/BALSAMIC:release/8_0_0Copy head branch name to clipboardAug 26, 2021

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Commits on May 20, 2021

• Fix/umi post process (#633)

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Commits on May 21, 2021

• Include all filtered variants in vcf-filtered-clinical not just PASSed (#635)

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Commits on May 25, 2021

• refactor align rules (#638)

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Commits on May 26, 2021

• Add samtools stats to QC steps (#639)

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• refactor vep, fastqc, mosdepth, and contest rules (#637)

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Commits on Jun 7, 2021

• Additional filter for tumor-normal calls in VarDict (#643)

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• Feat/deliver sv (#634)

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• Revert "Feat/deliver sv (#634)" (#646)

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• Second try: Feat/deliver sv (#647)

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Commits on Jun 14, 2021

• Add vcf2cytosure as dependency (#650)

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• cleanup unused container conda (#649)

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• Avoid running pytest when changelog or docs are updated (#651)

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Commits on Jun 15, 2021

• add git to containers (#652)

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Commits on Jun 28, 2021

• add purecn dependencies (#657)

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Commits on Jun 29, 2021

• Fix/issue 601 (#659)

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Commits on Jul 1, 2021

• add purecn in configs

  

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• refactor cnvkit single rule

  

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Commits on Jul 5, 2021

• cnvkit refactor changelog (#663)

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• Update GNOMAD URL [Issue 664] (#665)

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• Add Delly somatic SV caller [issue 644 ] (#645)

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• Update CODEOWNERS (#667)

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Commits on Jul 9, 2021

• Update docs to add reference section in FAQ

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• Update changelog

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• changelog

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• changelog

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• chanloge

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• Update FAQs.rst

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• Update FAQs.rst code blocks

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• Update FAQs.rst

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• Update FAQs highlights

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• Update FAQs highlights

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• Merge branch 'develop' into update/docs_FAQ_ascat

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• Merge branch 'update/docs_FAQ_ascat' into develop

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Commits on Jul 12, 2021

• add ascatngs as submodule and fixing tests (#668)

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• Merge remote-tracking branch 'origin/develop' into release/8_0_0

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• Removed the install.sh script [issue #655] (#676)

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• Merge remote-tracking branch 'origin/develop' into release/8_0_0

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Commits on Jul 14, 2021

• Optimize TMB calculation (#677)

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• Merge remote-tracking branch 'origin/master' into develop

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• Merge remote-tracking branch 'origin/develop' into release/8_0_0

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Commits on Jul 19, 2021

• Feat/delly tumor only rule (#681)

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• Add ascat reference download (#682)

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• Merge remote-tracking branch 'origin/develop' into release/8_0_0

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Commits on Jul 20, 2021

• Fix/ascat reference 20210720 (#691)

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Commits on Jul 22, 2021

• Merge remote-tracking branch 'origin/develop' into release/8_0_0

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Commits on Jul 23, 2021

• Feat/ascat download container (#689)

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Commits on Aug 2, 2021

• Fix/delly run (#698)

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• Doc/update sentieon info (#697)

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Commits on Aug 11, 2021

• Refactor/cnvkit single (#700)

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• fixed links for ascatngs documentation (#702)

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Commits on Aug 12, 2021

• Add ascat tumor normal rule (#699)

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Commits on Aug 17, 2021

• fix space in reference json (#705)

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Commits on Aug 18, 2021

• Fix/All containers´ performance improvements and fix for varcall_py36 container build (#706)

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Commits on Aug 19, 2021

• Merge remote-tracking branch 'origin/develop' into release/8_0_0

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• Feat/manta convert inversions (#710)

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• Merge remote-tracking branch 'origin/develop' into release/8_0_0

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Commits on Aug 20, 2021

• Refactor/umi variantcalling snakemake rules (#701)

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• refactor annotation rules according snakemake git etiquette (#696)

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• Refactor/rule cnvkit paired (#693)

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• update snakemake to v6.5.3 (#678)

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• Feat: generalize ascat, delly, and manta (#708)

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Commits on Aug 23, 2021

• refactor quality control rules (#712)

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Commits on Aug 24, 2021

• Refactor bioinfo tools version parsing (#713)

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• Feat: codeowner (#715)

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• Refactor/params to constants (#714)

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• merge develop

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Commits on Aug 25, 2021

• Feat/use black lint (#716)

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• Merge branch 'develop' into release/8_0_0

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