add nextflow d30e48d

nextflow/validation/await.sh

@@ -0,0 +1,41 @@
+#!/bin/bash
+set -eu
+
+TIMEOUT=3600    # terminate after one hour
+KEEPALIVE=480   # time after which print an output to keep alive travis
+
+# launch main command to await  
+( "$@" | tee stdout.log ) &
+pid=$!
+
+# make sure to terminate target command on exit
+trap "kill $pid" TERM INT USR1 USR2
+
+# monitor task execution 
+begin=$(date +%s)
+size=0
+while kill -0 $pid > /dev/null 2>&1; do 
+    sleep 1
+
+    # continue to await if there's a change 
+    # in the stdout file 
+    ### BSD current=$(stat -f%z stdout.log)
+    current=$(stat -c '%s' stdout.log)
+    if [[ $current != $size ]]; then
+      size=$current
+      begin=$(date +%s)
+      continue
+    fi
+
+    # kill the execution if it's taking too 
+    # much time without producing any output
+    now=$(date +%s)
+    delta=$((now-begin))
+    if ((delta>=$TIMEOUT)); then
+        echo Taking too long ... killing it!
+        kill $pid
+        exit 1
+    elif ((delta>=$KEEPALIVE)); then    
+        echo "[keep alive]"
+    fi  
+done