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Module/jabba/1.0#179

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ppararaj wants to merge 88 commits intomasterLCR-BCCRC/lcr-modules:masterfrom module/jabba/1.0LCR-BCCRC/lcr-modules:module/jabba/1.0Copy head branch name to clipboard

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Commits

Commits on Apr 2, 2021

• Add inital draft of jabba version 1.0

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• Added jabba reference environments

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• Added rules for generating Jabba GC RDS file.

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• Added rules for creating JaBba mappability reference file.

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Commits on Apr 6, 2021

• Add jabba environment yaml

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• Added fragcounter rules.

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Commits on Apr 8, 2021

• Added ref rules to create PAR region RDS file.

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• Increased request memory for download_ucsc_gc rule.

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• Increased requested memory of fragcounter rule.

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Commits on Apr 9, 2021

• Remove samtools environment.

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• Update env for dryclean and jabba rules.

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• Added fragcounter, dryclean rules.

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• Add JaBba source scripts.

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• Include seqlengths in GC, MAP, PAR GRanges.

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• Changed ucsc chrom sizes rule name.

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• Removed duplicate stringsAsFactors call.

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Commits on Apr 10, 2021

• Added custom fragcounter scripts to enable running chr-prefixed samples

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• Increase mem_mb for make_pon

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Commits on Apr 12, 2021

• Increased requested memory.

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• Use custom prepare_detergent.R

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• Use custom identify_germline.R

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• Mutliple changes to rules for generating coverage RDS

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• Use new rule names.

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• Add Changelog

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• Add JaBba install rule.

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Commits on Apr 14, 2021

• Add JaBbA default configs.

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• Use updated env yaml

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• Addded JaBbA run rule

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• Use Rscript to run JaBbA

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Commits on Apr 15, 2021

• Remove last TODO

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Commits on Apr 16, 2021

• Allow VCF and BEDPE SV inputs.

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Commits on Apr 17, 2021

• Syntax error in get_junc_file()

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• Changed junction inputs to simple symlinking

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Commits on Jun 15, 2021

• Copied FragCounter and DryClean installation rules.

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• Specified jabba env and PON normals in ref.

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Commits on Jun 16, 2021

• Moved PON rules into ref workflow.

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• Misc. scripts and files for creating PON in ref workflow.

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  5f523e8

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• Updated install rules.

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• Updated install rules in ref workflow.

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• Change require() to library() in install rules.

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• Make calls to reference subworkflow for PON files.

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• Use all GAMBL hg38 normals for PON.

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• Add grch37 normals for PON generation

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Commits on Jun 17, 2021

• Correctly finds src/ and etc/ ref directories.

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Commits on Jun 29, 2021

• Remove unused rules in localrules

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Commits on Jun 30, 2021

• Increased number of normals to include from 50 to 100.

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• Use correct germline marker filename.

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• Paramaterize manta and gridss junctions.

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• Update env file for merge_svs.R script.

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• Removed jabba run script from ref src directory because it is not used in ref workflow.

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• Rely on fragcounter, dryclean install rules in ref workflow.

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• Update normals used for PON.

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• Add SV merge script.

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• Remove unnecessary packages from loading.

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• Resources for merge_svs

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• More packages added to Jabba env.

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• Move installation rules back into jabba.smk

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• Fix minor syntax errors.

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Commits on Jul 1, 2021

• Multiple bug fixes.

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Commits on Jul 3, 2021

• Major fixes. Runs to completion on hg38.

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Commits on Jul 8, 2021

• Use gGnome functions for merging.

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Commits on Jul 12, 2021

• Update grch37 normals to use for PON/

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• Update fragcounter install and run rules.

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• Handle when filtering clobbers junctions.

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• Add logging to merge_sv rule

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• Remove custom fragcounter R scripts.

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Commits on Jul 13, 2021

• Fix empty.junc syntax error.

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Commits on Jul 15, 2021

• Handle when br object is empty.

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• Fix merge_svs bug. Move merge_svs to params to prevent full re-run.

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Commits on Aug 26, 2021

• Remove unused options in config.

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• Remove custom reference Rscripts

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• Remove reference to custom Rscripts.

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• Used morinlab dryclean fork repo

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Commits on Aug 27, 2021

• Added comments to JaBbA PON rules.

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• Use morinlab github fork.

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• Removed unused Rscripts from module src/

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Commits on Aug 28, 2021

• Add tier 3 category.

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Commits on Aug 29, 2021

• Updated env specs.

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• Handle empty/invalid SV VCFs. Remove old code.

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• Update install rules. Remove old code.

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Commits on Sep 20, 2021

• Add params opts

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• Remove old jabba run script.

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Commits on Oct 5, 2021

• Add missing libraries

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• Symlink .crai where appropriate.

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• Updated normals tables.

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• Process and use purity estimates for JaBbA.

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Commits on Nov 8, 2021

• Add capability to process GRIDSS2.0 VCFs

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Commits on Jan 31, 2022

• Merge branch 'master' into module/jabba/1.0

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