127 lines
2.5 KiB
Bash
Executable File
127 lines
2.5 KiB
Bash
Executable File
#!/bin/bash
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set -e
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get_abs_filename() {
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echo "$(cd "$(dirname "$1")" && pwd)/$(basename "$1")"
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}
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export NXF_IGNORE_WARN_DSL2=true
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export NXF_CMD=${NXF_CMD:-$(get_abs_filename ../launch.sh)}
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# disable ansi log to make log more readable
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export NXF_ANSI_LOG=false
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export NXF_DISABLE_CHECK_LATEST=true
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test_integration() {
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(
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cd "$1"
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sudo bash cleanup.sh
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cd checks
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bash run.sh
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)
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}
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test_e2e() {
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if [[ $TEST_SMOKE == true ]]; then
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echo Skipping tests since TEST_SMOKE flag is true
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exit 0
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fi
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#
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# Hello
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#
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git clone https://github.com/nextflow-io/hello
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(
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cd hello
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$NXF_CMD run .
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$NXF_CMD run . -resume
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)
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#
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# RNASEQ-NF
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#
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echo nextflow-io/rnaseq-nf
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[[ $TOWER_ACCESS_TOKEN ]] && OPTS='-with-tower' || OPTS=''
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$NXF_CMD run nextflow-io/rnaseq-nf -with-docker $OPTS
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$NXF_CMD run nextflow-io/rnaseq-nf -with-docker $OPTS -resume
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}
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#
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# Integration tests
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#
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if [[ $TEST_MODE == 'test_integration' ]]; then
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export NXF_SYNTAX_PARSER=v1
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test_integration ../tests/
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test_integration ../tests-v1/
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test_e2e
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fi
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#
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# Integration tests (strict syntax)
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#
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if [[ $TEST_MODE == 'test_parser_v2' ]]; then
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export NXF_SYNTAX_PARSER=v2
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test_integration ../tests/
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test_e2e
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fi
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#
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# Documentation tests
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#
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if [[ $TEST_MODE == 'test_docs' ]]; then
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(
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echo "Documentation tests"
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cd ../docs/snippets/
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bash test.sh
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)
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fi
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#
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# AWS Batch tests
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#
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if [[ $TEST_MODE == 'test_aws' ]]; then
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if [ "$AWS_ACCESS_KEY_ID" ]; then
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echo "AWS batch tests"
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bash awsbatch.sh
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else
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echo "::warning file=$0,line=$LINENO::Missing AWS_ACCESS_KEY_ID variable -- Skipping AWS Batch tests"
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fi
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fi
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#
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# Azure Batch tests
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#
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if [[ $TEST_MODE == 'test_azure' ]]; then
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if [ "$AZURE_BATCH_ACCOUNT_KEY" ]; then
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echo "Azure batch tests"
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bash azure.sh
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else
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echo "::warning file=$0,line=$LINENO::Missing AZURE_BATCH_ACCOUNT_KEY variable -- Skipping Azure Batch tests"
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fi
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fi
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#
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# Google Batch
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#
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if [[ $TEST_MODE == 'test_google' ]]; then
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if [ "$GOOGLE_SECRET" ]; then
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echo "Google Batch tests"
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bash google.sh
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else
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echo "::warning file=$0,line=$LINENO::Missing GOOGLE_SECRET variable -- Skipping Google Batch tests"
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fi
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fi
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#
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# Wave
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#
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if [[ $TEST_MODE == 'test_wave' ]]; then
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if [ "$TOWER_ACCESS_TOKEN" ]; then
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echo "Wave tests"
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bash wave.sh
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else
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echo "::warning file=$0,line=$LINENO::Missing TOWER_ACCESS_TOKEN variable -- Skipping Wave tests"
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fi
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fi
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