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2018-12-19link: introduce high-level linking functionsJustin Bedo
2018-12-10bowtie: initJustin Bedo
2018-11-29Revert "test-tnpair: avoid gridss.call while it's broken"l-d-s
This reverts commit 01401aaee74dac39e0502688654ef02771a88cd7.
2018-11-15test-tnpair: avoid gridss.call while it's brokenl-d-s
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.
2018-10-25Improve type safety of samtools-mergeJustin Bedo
2018-10-05implement typesJustin Bedo
2018-10-04Refactor referencesJustin Bedo
2018-10-04Add def function to simplify overridesJustin Bedo
2018-10-04Refactor to use bionix tree directlyJustin Bedo
2018-09-26Add flagstat and fastqcJustin Bedo
2018-09-26refactor, add mosdepth, and fixes for bwaJustin Bedo
2018-09-24use a map in the test pipelineJustin Bedo
2018-09-24Working test-tnpairl-d-s
2018-09-20Add example TNPairJustin Bedo
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