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Module/jabba/1.0 #179
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Module/jabba/1.0 #179
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ffed863
Add inital draft of jabba version 1.0
ppararaj bcf0852
Added jabba reference environments
ppararaj b0294bf
Added rules for generating Jabba GC RDS file.
ppararaj fe52350
Added rules for creating JaBba mappability reference file.
ppararaj 97f90e0
Add jabba environment yaml
ppararaj 5639972
Added fragcounter rules.
ppararaj fd725a9
Added ref rules to create PAR region RDS file.
ppararaj dab2c97
Increased request memory for download_ucsc_gc rule.
ppararaj 249a714
Increased requested memory of fragcounter rule.
ppararaj c11c136
Remove samtools environment.
ppararaj deb2afe
Update env for dryclean and jabba rules.
ppararaj d1257e9
Added fragcounter, dryclean rules.
ppararaj d97f0cb
Add JaBba source scripts.
ppararaj b8d9269
Include seqlengths in GC, MAP, PAR GRanges.
ppararaj 129831b
Changed ucsc chrom sizes rule name.
ppararaj 18221c3
Removed duplicate stringsAsFactors call.
ppararaj 6920c9e
Added custom fragcounter scripts to enable running chr-prefixed samples
ppararaj c055ef4
Increase mem_mb for make_pon
ppararaj 5801f1b
Increased requested memory.
ppararaj f40bd58
Use custom prepare_detergent.R
ppararaj 51d1dc7
Use custom identify_germline.R
ppararaj 6b9753c
Mutliple changes to rules for generating coverage RDS
ppararaj 093cf6f
Use new rule names.
ppararaj 1019876
Add Changelog
ppararaj 5ef8f73
Add JaBba install rule.
ppararaj 3116ddd
Add JaBbA default configs.
ppararaj 3e334ad
Use updated env yaml
ppararaj 7d50ad5
Addded JaBbA run rule
ppararaj e65c784
Use Rscript to run JaBbA
ppararaj eb8bf41
Remove last TODO
ppararaj f21db6c
Allow VCF and BEDPE SV inputs.
ppararaj 29c1104
Syntax error in get_junc_file()
ppararaj 0f940c8
Changed junction inputs to simple symlinking
ppararaj 62094e1
Copied FragCounter and DryClean installation rules.
ppararaj 85f9292
Specified jabba env and PON normals in ref.
ppararaj 7da5ce4
Moved PON rules into ref workflow.
ppararaj 5f523e8
Misc. scripts and files for creating PON in ref workflow.
ppararaj 9d0befb
Updated install rules.
ppararaj 49b3346
Updated install rules in ref workflow.
ppararaj 66f09b5
Change require() to library() in install rules.
ppararaj a5d20d3
Make calls to reference subworkflow for PON files.
ppararaj 081ac50
Use all GAMBL hg38 normals for PON.
ppararaj a94c6a8
Add grch37 normals for PON generation
ppararaj 6f6ece4
Correctly finds src/ and etc/ ref directories.
ppararaj 9227ff8
Remove unused rules in localrules
ppararaj ac59f77
Increased number of normals to include from 50 to 100.
ppararaj 7dd3520
Use correct germline marker filename.
ppararaj ffaba0e
Paramaterize manta and gridss junctions.
ppararaj 862e847
Update env file for merge_svs.R script.
ppararaj c447ccb
Removed jabba run script from ref src directory because it is not use…
ppararaj 50115df
Rely on fragcounter, dryclean install rules in ref workflow.
ppararaj b9accd2
Update normals used for PON.
ppararaj d21b022
Add SV merge script.
ppararaj 9dd419e
Remove unnecessary packages from loading.
ppararaj 8f3aa48
Resources for merge_svs
ppararaj 1a99647
More packages added to Jabba env.
ppararaj a708b7b
Move installation rules back into jabba.smk
ppararaj 5359e0e
Fix minor syntax errors.
ppararaj 3d1add7
Multiple bug fixes.
ppararaj 78a75d4
Major fixes. Runs to completion on hg38.
ppararaj c07bece
Use gGnome functions for merging.
ppararaj 6840cc7
Update grch37 normals to use for PON/
ppararaj f65d1dc
Update fragcounter install and run rules.
ppararaj 175b6fd
Handle when filtering clobbers junctions.
ppararaj ec1ddaa
Add logging to merge_sv rule
ppararaj fc792bb
Remove custom fragcounter R scripts.
ppararaj 3956783
Fix empty.junc syntax error.
ppararaj b59a8ee
Handle when br object is empty.
ppararaj 1d86bde
Fix merge_svs bug. Move merge_svs to params to prevent full re-run.
ppararaj c280ae9
Remove unused options in config.
ppararaj dae74fd
Remove custom reference Rscripts
ppararaj db7471b
Remove reference to custom Rscripts.
ppararaj aa0bfc1
Used morinlab dryclean fork repo
ppararaj 0f74492
Added comments to JaBbA PON rules.
ppararaj c5fd1a3
Use morinlab github fork.
ppararaj 9c56f07
Removed unused Rscripts from module src/
ppararaj 98447ba
Add tier 3 category.
ppararaj 6e3d57c
Updated env specs.
ppararaj fbfe6b4
Handle empty/invalid SV VCFs. Remove old code.
ppararaj 515cb83
Update install rules. Remove old code.
ppararaj 63c4431
Add params opts
ppararaj f9977b8
Remove old jabba run script.
ppararaj 2eb6217
Add missing libraries
ppararaj c8fc456
Symlink .crai where appropriate.
ppararaj 09cfafe
Updated normals tables.
ppararaj aacbc47
Process and use purity estimates for JaBbA.
ppararaj daeb9a4
Add capability to process GRIDSS2.0 VCFs
ppararaj d6603a5
Merge branch 'master' into module/jabba/1.0
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I think this bedtools got accidentally dropped, but otherwise looks good
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It appeared to be duplicated. There's an entry for bedtools above.
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I see it, thanks! So everything was pushed in this PR and this is the working version?