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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
2019-04-12minimap2: initJustin Bedo
2019-04-08grids: add function to include assemblies with annotated VCFJustin Bedo
2019-04-08bowtie: sort the output to ensure determinismJustin Bedo
2019-04-07modify outputs to ensure determinismJustin Bedo
2019-04-07update stage names to include bionix- prefixJustin Bedo
2019-03-28gridss: less chatty logsJustin Bedo
2019-03-28gridss: 2.0.0 → 2.2.2Justin Bedo
2019-03-22cnvkit: add scatter plotsJustin Bedo
2019-03-22cnvkit: copy less filesJustin Bedo
2019-03-15add multicore passthru flagJustin Bedo
2019-03-13mosdepth: fix broken pkg link for mosdepth sourceJustin Bedo
2019-03-06api docs: init GRIDSSJustin Bedo
2019-03-06api doc: init fastqcJustin Bedo
2019-03-06api docs: init facetsJustin Bedo
2019-03-06api docs: init CNVkitJustin Bedo
2019-03-06api docs: init ascatNGSJustin Bedo
2019-03-06api docs: fix bwa type annotationsJustin Bedo
2019-03-06api docs: init bowtieJustin Bedo
2019-03-06draft API docs for BWA and strelkaJustin Bedo
2019-03-01ascat: initJustin Bedo
2019-02-11snpeff: parameterise heap size and default to 31gJustin Bedo
2019-01-17strelka-callSomatic: remove superfluous gzip dependencyJustin Bedo
2019-01-17compression: refactor compression frameworkJustin Bedo
2019-01-17strelka: refactor vcf extractionJustin Bedo
2019-01-16strelka: split out vcfsJustin Bedo
2019-01-15strelka: add germline callingJustin Bedo
2019-01-14cnvkit: fix annotation bugJustin Bedo
2019-01-13snpeff-dbnsfp: fix buildInputsJustin Bedo
2019-01-13snpeff: fix dbnsfpJustin Bedo
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