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2019-01-08snpeff: initJustin Bedo
2019-01-03samtools-fixmate: default MS tag annotation to trueJustin Bedo
2018-12-21qsub: capture stderr and stdout jointlyJustin Bedo
2018-12-20README: add tnpair example to examples sectionJustin Bedo
2018-12-20qsub: bugfix with printing jobid for debuggingJustin Bedo
2018-12-19examples: update call.nix to use new pipe functionJustin Bedo
2018-12-19examples: added example tumour-normal calling pipeline scriptJustin Bedo
2018-12-19bionix: export nixpkgs.lib as bionix.libJustin Bedo
2018-12-19gridss: simplify preprocessing and rewrite using new pipe functionJustin Bedo
2018-12-19link: introduce high-level linking functionsJustin Bedo
2018-12-19qsub: echo out PBS_NODE_ID to ease debuggingJustin Bedo
2018-12-18pipe: fix bugJustin Bedo
2018-12-18pipe: reverse function compositionJustin Bedo
2018-12-18qsub: refactor overridingJustin Bedo
2018-12-12Merge branch 'master' of https://github.com/PapenfussLab/bionixl-d-s
2018-12-12gridss: call identifyVariants through bionix treeJustin Bedo
2018-12-12Merge branch 'master' of https://github.com/PapenfussLab/bionixl-d-s
2018-12-12gridss: refactor identify & annotate variantsJustin Bedo
2018-12-11Merge branch 'master' of https://github.com/PapenfussLab/bionixl-d-s
2018-12-11samtools-sort: fix reversed link for identity sortJustin Bedo
2018-12-11gridss: fix softClipsToSplitReads after assemblyJustin Bedo
2018-12-11qsub: prefix directories to prevent cleanup deleting top level dirJustin Bedo
2018-12-10gridss: add java heapSize arguments.l-d-s
2018-12-10qsub: fix $TMPDIR locationJustin Bedo
2018-12-10bowtie: initJustin Bedo
2018-12-10gridss: fix tmpdir bug.l-d-s
2018-12-06gridss: remove redundant collectGridssMetricsl-d-s
2018-11-29Correct argument for gridss option filel-d-s
2018-11-29gridss: fix for nix installations outside of /nixJustin Bedo
2018-11-29Revert "test-tnpair: avoid gridss.call while it's broken"l-d-s
This reverts commit 01401aaee74dac39e0502688654ef02771a88cd7.
2018-11-27Add licenceJustin Bedo
2018-11-27Expand README and add simple example pipelineJustin Bedo
2018-11-26qsub: output non-retryable errorsJustin Bedo
2018-11-26qsub: let sleep timing be configurableJustin Bedo
2018-11-26qsub: retry qsub if requestedJustin Bedo
2018-11-26Merge branch 'master' of https://github.com/PapenfussLab/bionixl-d-s
2018-11-26Also need config for 'assemble' step.l-d-s
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
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