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2018-10-29Split gridss into constituentsJustin Bedo
Wrap each individual command for GRIDSS so that bionix executed the pipeline rather than GRIDSS. This patch introduces a "call" function that executed the whole pipeline in bionix on an arbitrary BAM file. Resolves #10.
2018-10-29bwa-mem: BWA output is query name sortedJustin Bedo
2018-10-29init: samtools-markdupJustin Bedo
2018-10-29init: samtools-fixmateJustin Bedo
2018-10-26init: mutectJustin Bedo
2018-10-26init: samtools-dictJustin Bedo
2018-10-26init: cosmic & dbsnp for grch38Justin Bedo
2018-10-25Improve type safety of samtools-mergeJustin Bedo
2018-10-25Simplify types for sortingJustin Bedo
2018-10-24Merge branch 'master' of https://github.com/PapenfussLab/bionixl-d-s
2018-10-24Add merge to samtools.l-d-s
2018-10-24Simplify test expressionJustin Bedo
2018-10-24Fix platypus bugJustin Bedo
2018-10-23Allow building bwa-mem with one coreJustin Bedo
2018-10-23Simplify infercnv-appJustin Bedo
2018-10-23Wrap inferCNVJustin Bedo
Resolves #8
2018-10-22name qsub with name of derivation: fixes #7Justin Bedo
2018-10-17rename sigterm patchJustin Bedo
2018-10-09Simplify default to error in typesJustin Bedo
2018-10-08Add identity to compression functionsJustin Bedo
2018-10-08Fix type in samtools-viewJustin Bedo
2018-10-05implement typesJustin Bedo
2018-10-04Add defQsub functionJustin Bedo
2018-10-04Refactor referencesJustin Bedo
2018-10-04Add def function to simplify overridesJustin Bedo
2018-10-04Add qsub function to override all attributesJustin Bedo
2018-10-04Refactor to use bionix tree directlyJustin Bedo
2018-10-04add patch for nix to send SIGTERM instead of SIGKILLJustin Bedo
2018-10-04Fix typo in reference nameJustin Bedo
2018-10-04Stuff to match & points of differencel-d-s
2018-10-03Use http rather than ftp for mm10l-d-s
2018-10-03fix indenting and syntax errorJustin Bedo
2018-10-03refactor reference location to libJustin Bedo
2018-10-03Add GRCm38-p6Justin Bedo
2018-10-03sha256 hash for mm10l-d-s
2018-10-02Add mm10 reference (UCSC)l-d-s
2018-09-28Add crumbleJustin Bedo
2018-09-28Change mosdepth plotting to multisampleJustin Bedo
2018-09-28Improve cleanup of qsubJustin Bedo
2018-09-28Fix missing index for mosdepthJustin Bedo
2018-09-27Allow flag passing to bwa indexJustin Bedo
2018-09-27Allow changing tmpdir for qsubJustin Bedo
2018-09-26Missing GRIDSS filesJustin Bedo
2018-09-26Add GRIDSSJustin Bedo
2018-09-26move bwa index to parametersJustin Bedo
2018-09-26Fix mosdepthJustin Bedo
2018-09-26Fix fastqcJustin Bedo
2018-09-26fix qsub expressionJustin Bedo
2018-09-26Add qsub to bionix top levelJustin Bedo
2018-09-26Add flagstat and fastqcJustin Bedo
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