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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
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
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