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2018-11-23qsub: update to check job_state fieldJustin Bedo
2018-11-23qsub: be more specific with qstat pollingJustin Bedo
2018-11-22Merge branch 'master' of https://github.com/PapenfussLab/bionixl-d-s
2018-11-22gridss: restructure gridss pipelineJustin Bedo
2018-11-22samtools-sort: handle missing 'none' sorting caseJustin Bedo
2018-11-22gridss: fix configure file optional string errorJustin Bedo
2018-11-20Add some typed fetchurl functionsJustin Bedo
2018-11-15Fix up gridss config file.l-d-s
2018-11-15test-tnpair: avoid gridss.call while it's brokenl-d-s
2018-11-15gridss.softClipsToSplitReads: sort -> sortingl-d-s
2018-11-15Syntax.l-d-s
2018-11-15Ignore temporary files.l-d-s
2018-11-15Need to test config != nulll-d-s
2018-11-15Merge branch 'master' of https://github.com/PapenfussLab/bionixl-d-s
2018-11-15Ignore .DS_Storel-d-s
2018-11-15gridss.softClipsToSplitReads: sort ordering is not preservedJustin Bedo
NB: this breaks gridss.preprocessBam
2018-11-14Add ensembl mouse transcriptomeJustin Bedo
2018-11-13Merge branch 'master' of https://github.com/PapenfussLab/bionixl-d-s
2018-11-12Attempt to integrate config file into GRIDSS stagel-d-s
2018-11-12Function to great ini-style gridss config file.l-d-s
2018-11-07Fix to gridss.l-d-s
2018-11-07Add bwa to softClipsToSplitReadsl-d-s
2018-11-02Allow bwa-mem to take gzipped fastq inputsJustin Bedo
2018-11-02kallisto: initJustin Bedo
2018-11-01samtools-sort: don't sort if already sortedJustin Bedo
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
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