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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
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
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