diff --git a/CHANGELOG.md b/CHANGELOG.md index 6c037d25021b4c1371cc388c1fda79696be19843..6d185a8f38d471f5d2e250c07b9c380d926b6a74 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,7 @@ version 2.2.0-dev --------------------------- + Add CCS workflow WDL files (ccs.wdl, lima.wdl, isoseq3.wdl). + Update TALON version to 4.4.2. ++ The statsPrefix input for umitools dedup is now optional. + Allow setting the `--emit-ref-confidence` flag for HaplotypeCaller. + Add `--output-mode` flag to HaplotypeCaller. + Added rtg.Format and rtg.VcfEval tasks. diff --git a/umi-tools.wdl b/umi-tools.wdl index e684ef5aac68c6c9d6ae51e1bd363d48366f56ee..35d54299ff8425090e5beb408857ea7e994fc1f7 100644 --- a/umi-tools.wdl +++ b/umi-tools.wdl @@ -71,10 +71,10 @@ task Dedup { File inputBam File inputBamIndex String outputBamPath - String statsPrefix = "stats" + String? statsPrefix Boolean paired = true - String memory = "20G" + String memory = "5G" # Use a multi-package-container which includes umi_tools (0.5.5) and samtools (1.9) String dockerImage = "quay.io/biocontainers/mulled-v2-509311a44630c01d9cb7d2ac5727725f51ea43af:6089936aca6219b5bb5f54210ac5eb456c7503f2-0" @@ -88,7 +88,7 @@ task Dedup { umi_tools dedup \ --stdin ~{inputBam} \ --stdout ~{outputBamPath} \ - --output-stats ~{statsPrefix} \ + ~{"--output-stats " + statsPrefix} \ ~{true="--paired" false="" paired} samtools index ~{outputBamPath} ~{outputBamIndex} } @@ -96,9 +96,9 @@ task Dedup { output { File deduppedBam = outputBamPath File deduppedBamIndex = outputBamIndex - File editDistance = statsPrefix + "_edit_distance.tsv" - File umiStats = statsPrefix + "_per_umi.tsv" - File positionStats = statsPrefix + "_per_umi_per_position.tsv" + File? editDistance = statsPrefix + "_edit_distance.tsv" + File? umiStats = statsPrefix + "_per_umi.tsv" + File? positionStats = statsPrefix + "_per_umi_per_position.tsv" } runtime {