diff --git a/CHANGELOG.md b/CHANGELOG.md index 7d5652fa9dd1846dfa6646d246fdcf9766bf95d0..fc71ca8e26ac3b48a4c08cb7285f4792a505b84b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,10 @@ that users understand how the changes affect the new version. version 2.1.0-dev --------------------------- ++ Make intervals optional for GATK CombineGVCFs ++ Updated biowdl-input-converter version. ++ GATK CombineGVCFs memory was tripled to prevent it from using a lot of CPU in + Garbage Collection mode. + Updated parameter_meta sections for Minimap2 and TranscriptClean to wdl-aid format. + Updated cores variable for TALON, the default is now 4. + Updated TALON to version 4.4. diff --git a/biowdl.wdl b/biowdl.wdl index f428a91fc3b0c719804c46b5aba326339187d908..e524ac6e5473a0f30219e30104d543cca6ecee99 100644 --- a/biowdl.wdl +++ b/biowdl.wdl @@ -31,7 +31,7 @@ task InputConverter { Boolean skipFileCheck=true Boolean checkFileMd5sums=false Boolean old=false - String dockerImage = "quay.io/biocontainers/biowdl-input-converter:0.2.0--py_0" + String dockerImage = "quay.io/biocontainers/biowdl-input-converter:0.2.1--py_0" } command <<< diff --git a/gatk.wdl b/gatk.wdl index 0ab30fc18de79b75e53ece5ba4ae3e768f3436ca..ce8d4c46c8a66f9c3d7ea5d94dc2bbd4246fa38c 100644 --- a/gatk.wdl +++ b/gatk.wdl @@ -95,14 +95,14 @@ task CombineGVCFs { input { Array[File]+ gvcfFiles Array[File]+ gvcfFilesIndex - Array[File]+ intervals + Array[File] intervals = [] String outputPath File referenceFasta File referenceFastaDict File referenceFastaFai - String memory = "12G" - String javaXmx = "4G" + String memory = "24G" + String javaXmx = "12G" String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0" } @@ -114,7 +114,7 @@ task CombineGVCFs { -R ~{referenceFasta} \ -O ~{outputPath} \ -V ~{sep=' -V ' gvcfFiles} \ - -L ~{sep=' -L ' intervals} + ~{true='-L' false='' length(intervals) > 0} ~{sep=' -L ' intervals} } output {