PIP-1234-pytest-wf (#50)

requirements.txt

@@ -0,0 +1,64 @@
+aadict==0.2.3
+argcomplete==1.11.1
+asset==0.6.13
+attrs==19.3.0
+autouri==0.1.4
+awscli==1.18.72
+boto3==1.13.22
+botocore==1.16.22
+cachetools==4.1.0
+caper==0.8.2.1
+certifi==2020.4.5.1
+cffi==1.14.0
+chardet==3.0.4
+colorama==0.4.3
+coloredlogs==11.3
+cryptography==2.9.2
+dateparser==0.7.4
+docker==4.2.1
+docutils==0.15.2
+filelock==3.0.12
+globre==0.1.5
+google-api-core==1.17.0
+google-auth==1.16.0
+google-cloud-core==1.3.0
+google-cloud-storage==1.28.1
+google-resumable-media==0.5.1
+googleapis-common-protos==1.52.0
+humanfriendly==8.2
+idna==2.9
+importlib-metadata==1.6.0
+jmespath==0.10.0
+jsonschema==3.2.0
+lark-parser==0.8.5
+miniwdl==0.7.4
+more-itertools==8.3.0
+packaging==20.4
+pluggy==0.13.1
+protobuf==3.12.2
+py==1.8.1
+pyasn1==0.4.8
+pyasn1-modules==0.2.8
+pycparser==2.20
+pygtail==0.11.1
+pyhocon==0.3.55
+pyOpenSSL==19.1.0
+pyparsing==2.4.7
+pyrsistent==0.16.0
+pytest==5.4.3
+pytest-workflow @ git+https://github.com/LUMC/pytest-workflow.git@4cbc3bb6b9840dafdfc584d62c1e7f9503f6291b
+python-dateutil==2.8.1
+python-json-logger==0.1.11
+pytz==2020.1
+PyYAML==5.3.1
+regex==2020.5.14
+requests==2.23.0
+rsa==3.4.2
+s3transfer==0.3.3
+six==1.15.0
+tzlocal==2.1
+urllib3==1.25.9
+wcwidth==0.2.3
+websocket-client==0.57.0
+xdg==4.0.1
+zipp==3.1.0

test/caper_run.sh

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+#!/bin/bash
+
+set -e
+
+echo "Running cromwell $CROMWELL, womtool $WOMTOOL and image $TAG"
+
+if [[ $# -eq 1 ]]; then
+    caper run $1 --docker $TAG --cromwell $CROMWELL --womtool $WOMTOOL --options ./test/cromwell_options.json -m metadata.json
+fi
+
+if [[ $# -eq 2 ]]; then
+    caper run $1 --docker $TAG --cromwell $CROMWELL --womtool $WOMTOOL -i $2 --options ./test/cromwell_options.json -m metadata.json
+fi

test/cromwell_options.json

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+{
+"default_runtime_attributes": {
+  "docker_user": "$EUID"
+  }
+}