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2019-12-20kallisto: attempt at making determinsticJustin Bedo
2019-12-20lumpy: fix error messageJustin Bedo
2019-12-18lumpy: initJustin Bedo
2019-12-17delly: missing fileJustin Bedo
2019-12-17manta: make multithreaded and apply execution contextJustin Bedo
2019-12-17delly: initJustin Bedo
2019-12-16manta: initJustin Bedo
2019-12-12octopus: fix incorrect error messageJustin Bedo
2019-12-05platypus: remove debugging codeJustin Bedo
2019-11-27gridss: 2.7.2 → 2.7.3Justin Bedo
2019-11-20gridss: 2.7.1 → 2.7.2Justin Bedo
2019-11-04gridss: 2.7.0 → 2.7.1Justin Bedo
2019-11-01gridss: 2.6.2 -> 2.7.0Justin Bedo
2019-09-25facets: assume sorted vcfJustin Bedo
2019-09-25gridss 2.6.0 → 2.6.2Justin Bedo
2019-09-10gridss: 2.5.2 -> 2.6.0Justin Bedo
2019-09-06strelka: default callSomatic to snvsJustin Bedo
2019-09-06strelka: also strip command line from outputJustin Bedo
2019-09-06cnvkit: use python2Justin Bedo
2019-09-06strelka: change outputs and taggingJustin Bedo
This resolves an issue where overriding the strelka derivations would lose the filetype tags.
2019-09-06xenomapper: initJustin Bedo
2019-09-06CNVkit: split into multiple outputsJustin Bedo
cnvkit: restructure out to link to multioutputs
2019-08-29CNVkit: merge into nixpkgsJustin Bedo
2019-08-29gridss: 2.5.1 -> 2.5.2Justin Bedo
2019-08-19snver: require labelled samplesJustin Bedo
SNVer does not extract sample names from the BAM files and labels the columns with the input file paths rather than sample names. We rename the paths to names.
2019-08-19snver: fix linkingJustin Bedo
2019-08-16mosdepth: fix renamingJustin Bedo
2019-08-15gridss: 2.5.0 -> 2.5.1Justin Bedo
2019-08-15hisat2: initJustin Bedo
2019-08-15SNVer: init 0.5.3Justin Bedo
2019-07-28gridss: 2.4.0 -> 2.5.0Justin Bedo
2019-07-03mosdepth-plot: allow selection of what to plotJustin Bedo
Previously global output was plotted. A new control flag allows specification of what to plot.
2019-07-03facets: fix execution environmentJustin Bedo
2019-07-03octopus: initial functionsJustin Bedo
2019-06-21gridss: 2.2.2 -> 2.4.0Justin Bedo
2019-06-21bwa-mem2: initJustin Bedo
2019-06-06Merge branch 'master' of https://github.com/PapenfussLab/bionixl-d-s
2019-06-06picard-markDuplicates: fix input and output typesl-d-s
2019-05-30picard-markDuplicates: Check for _any_ sorting of inputl-d-s
2019-05-30Add picard-markDuplicates - need to handle sorting ambiguity.l-d-s
2019-05-22Unested picard-markDuplicates.l-d-s
2019-05-21fastp: input filetypesJustin Bedo
2019-05-21fastp: split outputs and set filetypesJustin Bedo
2019-05-14strip: remove store paths from outputs to minimise closuresJustin Bedo
2019-05-09strelka: rewrite to use multiple outputsJustin Bedo
2019-05-09fastp: rename run to check for consistency with fastqcJustin Bedo
2019-05-02samtools-merge: detect correct sortingJustin Bedo
2019-05-01Add fastp.l-d-s
2019-04-17snap: initJustin Bedo
2019-04-12minimap2: typoJustin Bedo
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