diff --git a/CHANGELOG.md b/CHANGELOG.md index 121c876817134881b5ca408fc809cd90af236d80..a9329bf5e8eeeca3a1705c43ad389cca68f58ca1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,8 @@ that users understand how the changes affect the new version. version 5.0.0-dev --------------------------- ++ collect-columns: updated docker image to version 1.0.0 and added the + `sumOnDuplicateId` input (defaults to false). + survivor: replace integer boolean type to logical true or false value. + vt: Add option to ignore masked reference. + bcftools: add sorting and annotation diff --git a/collect-columns.wdl b/collect-columns.wdl index e4e3a948dc8665dd34837a43e43a046fb40e7037..fe41c5e897c0095792f94f27cfcf1716ca7874b9 100644 --- a/collect-columns.wdl +++ b/collect-columns.wdl @@ -29,13 +29,14 @@ task CollectColumns { Int? separator Array[String]? sampleNames Boolean header = false + Boolean sumOnDuplicateId = false Array[String]? additionalAttributes File? referenceGtf String? featureAttribute Int memoryGb = 4 + ceil(0.5 * length(inputTables)) Int timeMinutes = 10 - String dockerImage = "quay.io/biocontainers/collect-columns:0.2.0--py_1" + String dockerImage = "quay.io/biocontainers/collect-columns:1.0.0--py_0" } command { @@ -49,6 +50,7 @@ task CollectColumns { ~{"-s " + separator} \ ~{true="-n" false="" defined(sampleNames)} ~{sep=" " sampleNames} \ ~{true="-H" false="" header} \ + ~{true="-S" false="" sumOnDuplicateId} \ ~{true="-a" false="" defined(additionalAttributes)} ~{sep=" " additionalAttributes} \ ~{"-g " + referenceGtf} \ ~{"-F " + featureAttribute} @@ -72,6 +74,7 @@ task CollectColumns { separator: {description: "Equivalent to the -s option of collect-columns.", category: "advanced"} sampleNames: {description: "Equivalent to the -n option of collect-columns.", category: "advanced"} header: {description: "Equivalent to the -H flag of collect-columns.", category: "advanced"} + sumOnDuplicateId: {description: "Equivalent to the -S flag of collect-columns.", category: "advanced"} additionalAttributes: {description: "Equivalent to the -a option of collect-columns.", category: "advanced"} referenceGtf: {description: "Equivalent to the -g option of collect-columns.", category: "advanced"} featureAttribute: {description: "Equivalent to the -F option of collect-columns.", category: "advanced"}