diff --git a/CHANGELOG.md b/CHANGELOG.md index 6fe791f5a2ae1857cdbb787e094edd7e4807c70e..6c037d25021b4c1371cc388c1fda79696be19843 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,19 +11,21 @@ that users understand how the changes affect the new version. version 2.2.0-dev --------------------------- ++ Add CCS workflow WDL files (ccs.wdl, lima.wdl, isoseq3.wdl). ++ Update TALON version to 4.4.2. + Allow setting the `--emit-ref-confidence` flag for HaplotypeCaller. + Add `--output-mode` flag to HaplotypeCaller. + Added rtg.Format and rtg.VcfEval tasks. + Added gatk.SelectVariants and gatk.VariantFiltration tasks. + Fixed a bug where the output directory was not created for bwa.Kit. + Add vt task for variants normalization and decomposition. -+ Update WDL task Picard (Add task RenameSample) -+ Update WDL task Samtools (Add task FilterShortReadsBam) -+ Add WDL task for BCFtools (bcf to vcf) -+ Add WDL task for SURVIVOR (merge) -+ Update WDL task Manta (Add germline SV calling) -+ Add WDL task for Delly -+ Add WDL task for Clever (and Mate-Clever) ++ Update WDL task Picard (Add task RenameSample). ++ Update WDL task Samtools (Add task FilterShortReadsBam). ++ Add WDL task for BCFtools (bcf to vcf). ++ Add WDL task for SURVIVOR (merge). ++ Update WDL task Manta (Add germline SV calling). ++ Add WDL task for Delly. ++ Add WDL task for Clever (and Mate-Clever). + Add proper copyright headers to all WDL files. So the free software license is clear to end users who wish to adapt and modify. + Add pedigree input for HaplotypeCaller and GenotypeGVCFs. @@ -42,7 +44,7 @@ version 2.2.0-dev + Update parameter_meta for TALON, Centrifuge and Minimap2. + Centrifuge: Fix issue where Centrifuge Inspect did not get the correct index files location. + Add `minimumContigLength` input to PlotDenoisedCopyRatios and PlotModeledSegments. -+ Add `commonVariantSitesIndex` input to CollectAllelicCounts ++ Add `commonVariantSitesIndex` input to CollectAllelicCounts. + Centrifuge: Fix issue where Centrifuge could not locate index files. + Increase default memory of BWA mem to 32G (was 16G). + Add `memory` input to fastqc task. @@ -77,9 +79,9 @@ version 2.2.0-dev + Removed the "extraArgs" input from FilterMutectCalls. + Removed unused "verbose" and "quiet" inputs from multiqc. + Added parameter_meta sections to a variety of tasks. -+ Picard's BedToIntervalList outputPath input is now optional (with a default of "regions.interval_list") ++ Picard's BedToIntervalList outputPath input is now optional (with a default of "regions.interval_list"). + TALON: Fix SQLite error concerning database/disk space being full. -+ Update htseq to default image version 0.11.2 ++ Update htseq to default image version 0.11.2. + Update biowdl-input-converter in common.wdl to version 0.2.1. + Update TALON section to now include the new annotation file output, and add config file creation to the TALON task. + Removed unused inputs (trimPrimer and format) for cutadapt.