add nextflow d30e48d

This commit is contained in:
2026-04-29 23:01:54 +02:00
parent d0b12d668d
commit 97cc9058d3
2840 changed files with 730250 additions and 0 deletions

View File

@@ -0,0 +1,47 @@
#!/bin/bash
#
# Test agent output mode error handling (NXF_AGENT_MODE=true)
#
set -e
# Run workflow with agent mode enabled (expect failure)
NXF_AGENT_MODE=true $NXF_CMD -q run $NXF_SCRIPT > stdout.txt 2> stderr.txt && {
echo "ERROR: Workflow should have failed"
exit 1
}
# Verify agent output format contains error info
if ! grep -q '\[PIPELINE\]' stdout.txt; then
echo "ERROR: Missing [PIPELINE] in agent output"
cat stdout.txt
exit 1
fi
if ! grep -q '\[ERROR\]' stdout.txt; then
echo "ERROR: Missing [ERROR] in agent output"
cat stdout.txt
exit 1
fi
if ! grep -q '\[FAILED\]' stdout.txt; then
echo "ERROR: Missing [FAILED] in agent output"
cat stdout.txt
exit 1
fi
# Verify error contains exit code
if ! grep -q 'exit: 127' stdout.txt; then
echo "ERROR: Missing exit code in error output"
cat stdout.txt
exit 1
fi
# Verify error contains workdir
if ! grep -q 'workdir:' stdout.txt; then
echo "ERROR: Missing workdir in error output"
cat stdout.txt
exit 1
fi
echo "Agent error output mode test passed"