version 5.1.0 + Add the `highlyDiploidPercentage` and `somaticMinPuritySpread` inputs to the hmtools PURPLE task. + Add a task for fastp. + Add a task for picard CollectInsertSizeMetrics. + Increased the timeMinutes runtime attribute for manta (somatic and germline) to `2880`. + Add a task for GRIDSS somatic filtering. + Add a task to generate a panel of normals BED and BEDPE file for GRIDSS. + Add a task to filter a GRIDSS PON. + Add a task for delly somatic filtering. + Delly CallSV's `bamFile` and `bamIndex` inputs are not arrays of files, allowing for multiple samples to be included. + Add `samples` input to bcftools view to select samples included in the output vcf. + Add a separatorChar input to the tagUmi task. + Bug fix: Add space between flag and the value provided for macs2 + Add optional inputs to macs2, aiming to allow adhering to Encode ATACs-seq. Inputs added: + nomodel + gensz + extsize + shiftsize + pval_thres + bdg + keepdup + callsummits + Update samtools image to version 1.16. + Add targetsFile input for samtools View. + Mateclever's runtime attribute defaults were changed to: + memory: `"250GiB"` + timeMinutes: `2880` + Clever's Prediction task's runtime attribute defaults were changed to: + memory: `"80GiB"` + timeMinutes: `2200` + The GRIDSS AnnotateSvTypes task now also removes the second breakend of the breakpoints and single breakends. This will prepare the output better to be passed into survivor. + Updated SURVIVOR version to 1.0.7 + Add a combined samtools dict and samtools faidx task. + Add a BWA index task. + Move all memory notation to `KiB`, `MiB` and `GiB` from `K`, `M` and `G` previously. The WDL spec clearly distuingishes between SI and binary notations. Since Java always takes `K`, `M` and `G` to mean `KiB`, `MiB` and `GiB` this means java tasks such as GATK, FastQC and Picard will always receive enough memory now. + Purple's `somaticRainfallPlot` output is now optional and included in the `plots` output as well. + Bedtools coverage's timeMinutes now defaults to `320`. + Gridss' runtime attribute defaults were changed to: + jvmHeapSizeGb: `64` + nonJvmMemoryGb: `10` + threads: `12` + Virusbreakend's runtime attribute defaults were changed to: + threads: `12` + timeMinutes: `320` + Cobalt's timeMinutes now defaults to `480`. + Orange's timeMinutes now defaults to 10. + Sage's runtime attributes were changed to: + threads: `32` + javaXmx: `"16G"` + memory: `"20G"` + timeMinutes: `720` + Sambamba's runtimeMinutes nor defaults to `320`. + Added a task for CupGenerateReport. + Updated Cuppa to version 1.6. + Added a task for Gripss. + Fixed the HealthChecker task's determination of the `succeeded` output value. + Updated Linx to version 1.18. + Added a task for LinxVisualization. + Added a task for HMFtools Orange. + Added a task for HMFtools Pave. + Updated Purple to version 3.2. + Added plot and table outputs of Sage to task outputs. + Updated virus-interpreter to version 1.2. + Updated Peach to version 1.5. + Added a task to add SVTYPE annotations to GRIDSS results (`AnnotateSvTypes`). + The GRIDSS task will now run tabix separately if GRIDSS doesn't produce a vcf index. + Add a script to subtract UMI's from the read name and add them as a BAM tag for each BAM record. The script is in umi.BamReadNameToUmiTag. + Add fgbio.AnnotateBamWithUmis. + Add picard.UmiAwareMarkDuplicatesWithMateCigar. + Added a task for SnpEff. + Adjusted runtime settings for sambamba Markdup. + Added a task for sambamba Flagstat. + Added a task for Picard CollectWgsMetrics. + Added a task for Peach. + Added tasks for HMFtools: + Amber + Cobalt + Cuppa + CuppaChart + GripssApplicationKt + GripssHardFilterApplicationKt + HealthChecker + Linx + Protect + Purple + Sage + VirusInterpreter + Added a task for VirusBreakend. + Added a task for GridssAnnotateVcfRepeatmasker. + Bumped GRIDSS version to 2.12.2. + Adjusted GRIDSS runtime settings. + Added optional inputs to GRIDSS: + blacklistBed + gridssProperties + Added a task for GRIDSS AnnotateInsertedSequence. + Added a task for ExtractSigPredictHRD. + Added a task for DeconstructSigs. + Added option useSoftclippingForSupplementary (default false) to BWA mem. + Adjusted BWA mem runtime settings. + Added a task for bedtools coverage. + Added a task for bcftools filter. + Adjusted runtime settings for bcftools annotate. + Added optional inputs to bcftools annotate: + inputFileIndex + annsFileIndex + Update parameter_meta for macs2 + Add sample position in array task.