test-ci.sh

#!/bin/bash
#
# setup env for integration tests
#
TEST_JDK=${TEST_JDK:=11}
X_BRANCH=${TRAVIS_BRANCH:-${CIRCLE_BRANCH:-'master'}}
X_PULL_REQUEST=${TRAVIS_PULL_REQUEST:-false}
## handle github variables
[[ $GITHUB_REF ]] && X_BRANCH=$(echo $GITHUB_REF | awk '{n=split($1,A,"/"); print A[n]}')
[[ $GITHUB_EVENT_NAME == pull_request ]] && X_PULL_REQUEST=true

if [[ $X_PULL_REQUEST != false ]] && [ ${TEST_JDK} -ne 11 ]; then
  echo "Skipping integration tests on PR and JDK != 11"
  exit 0
fi

if [[ $X_BRANCH != master && $X_BRANCH != testing ]] && [ ${TEST_JDK:=11} -ne 11 ]; then
  echo "Integration tests are only executed on branch 'master' or 'testing' for JDK != 11"
  exit 0
fi

export WITH_DOCKER='-with-docker'
export NXF_PLUGINS_DIR=$PWD/build/plugins
export NXF_CMD=$PWD/nextflow;
export CAPSULE_LOG=none
export TEST_JDK
export TEST_MODE

unset JAVA_TOOL_OPTIONS # this variable mess-up Capsule loader Java version parsing
(
 $NXF_CMD info
 cd validation
 bash -x test.sh
)