diff --git a/.travis.yml b/.travis.yml index 4065d1cb15dd8c5d625c7ed43043955d1b7bd8a8..7019e07a4fde725b05e6e8d355f3f9574e81d428 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,9 +1,8 @@ language: java script: - set -e -- export CROMWELL_VERSION=34 -# - wget https://github.com/broadinstitute/cromwell/releases/download/$CROMWELL_VERSION/womtool-$CROMWELL_VERSION.jar -- wget https://barmsijs.lumc.nl/womtool-35-a7ae2d8-SNAP.jar +- export CROMWELL_VERSION=35 +- wget https://github.com/broadinstitute/cromwell/releases/download/$CROMWELL_VERSION/womtool-$CROMWELL_VERSION.jar - for F in `find -name "*.wdl"`; do echo $F; java -jar womtool-*.jar validate $F; done - 'if [ "$TRAVIS_PULL_REQUEST" != "false" ]; then git submodule foreach --recursive git checkout $TRAVIS_BRANCH && git submodule foreach --recursive git pull; fi' - "git diff --exit-code || (echo ERROR: Git changes detected. Please update submodules && exit 1)" diff --git a/biopet/sampleconfig.wdl b/biopet/sampleconfig.wdl index 3e530ac5c6df802af99564d0af537cb19140ebdc..c8e30e4ba4542f9a040666465ef64cb2aa18938b 100644 --- a/biopet/sampleconfig.wdl +++ b/biopet/sampleconfig.wdl @@ -110,7 +110,7 @@ task CaseControl { output { File outputFile = outputPath - Array[CaseControl] caseControls = read_json(outputFile) + CaseControls caseControls = read_json(outputFile) } runtime { diff --git a/common.wdl b/common.wdl index c618cbfdf7d155d6b783f3d8bb8b8dc201fd8d0e..289113d38816ba790d121a365f4f08d0f5cca362 100644 --- a/common.wdl +++ b/common.wdl @@ -170,3 +170,7 @@ struct CaseControl { String controlName IndexedBamFile controlBam } + +struct CaseControls { + Array[CaseControl] caseControls +}