add nextflow d30e48d

nextflow/validation/test.sh

@@ -0,0 +1,126 @@
+#!/bin/bash 
+set -e 
+
+get_abs_filename() {
+  echo "$(cd "$(dirname "$1")" && pwd)/$(basename "$1")"
+}
+
+export NXF_IGNORE_WARN_DSL2=true
+export NXF_CMD=${NXF_CMD:-$(get_abs_filename ../launch.sh)}
+# disable ansi log to make log more readable
+export NXF_ANSI_LOG=false
+export NXF_DISABLE_CHECK_LATEST=true
+
+test_integration() {
+    (
+      cd "$1"
+      sudo bash cleanup.sh
+      cd checks
+      bash run.sh
+    )
+}
+
+test_e2e() {
+    if [[ $TEST_SMOKE == true ]]; then
+      echo Skipping tests since TEST_SMOKE flag is true
+      exit 0
+    fi
+
+    #
+    # Hello
+    #
+    git clone https://github.com/nextflow-io/hello
+    (
+      cd hello
+      $NXF_CMD run .
+      $NXF_CMD run . -resume
+    )
+
+    #
+    # RNASEQ-NF
+    #
+    echo nextflow-io/rnaseq-nf
+    [[ $TOWER_ACCESS_TOKEN ]] && OPTS='-with-tower' || OPTS=''
+    $NXF_CMD run nextflow-io/rnaseq-nf -with-docker $OPTS
+    $NXF_CMD run nextflow-io/rnaseq-nf -with-docker $OPTS -resume
+}
+
+#
+# Integration tests
+#
+if [[ $TEST_MODE == 'test_integration' ]]; then
+  export NXF_SYNTAX_PARSER=v1
+  test_integration ../tests/
+  test_integration ../tests-v1/
+  test_e2e
+fi
+
+#
+# Integration tests (strict syntax)
+#
+if [[ $TEST_MODE == 'test_parser_v2' ]]; then
+  export NXF_SYNTAX_PARSER=v2
+  test_integration ../tests/
+  test_e2e
+fi
+
+#
+# Documentation tests
+#
+if [[ $TEST_MODE == 'test_docs' ]]; then
+
+    (
+      echo "Documentation tests"
+      cd ../docs/snippets/
+      bash test.sh
+    )
+
+fi
+
+#
+# AWS Batch tests
+#
+if [[ $TEST_MODE == 'test_aws' ]]; then
+    if [ "$AWS_ACCESS_KEY_ID" ]; then
+      echo "AWS batch tests"
+      bash awsbatch.sh
+    else
+      echo "::warning file=$0,line=$LINENO::Missing AWS_ACCESS_KEY_ID variable -- Skipping AWS Batch tests"
+    fi
+fi
+
+#
+# Azure Batch tests
+#
+if [[ $TEST_MODE == 'test_azure' ]]; then
+    if [ "$AZURE_BATCH_ACCOUNT_KEY" ]; then
+      echo "Azure batch tests"
+      bash azure.sh
+    else
+      echo "::warning file=$0,line=$LINENO::Missing AZURE_BATCH_ACCOUNT_KEY variable -- Skipping Azure Batch tests"
+    fi
+fi
+
+#
+# Google Batch
+#
+if [[ $TEST_MODE == 'test_google' ]]; then
+    if [ "$GOOGLE_SECRET" ]; then
+      echo "Google Batch tests"
+      bash google.sh
+    else
+      echo "::warning file=$0,line=$LINENO::Missing GOOGLE_SECRET variable -- Skipping Google Batch tests"
+    fi
+fi
+
+#
+# Wave
+#
+if [[ $TEST_MODE == 'test_wave' ]]; then
+    if [ "$TOWER_ACCESS_TOKEN" ]; then
+      echo "Wave tests"
+      bash wave.sh
+    else
+      echo "::warning file=$0,line=$LINENO::Missing TOWER_ACCESS_TOKEN variable -- Skipping Wave tests"
+    fi
+fi