add nextflow d30e48d

nextflow/docs/snippets/test.sh

@@ -0,0 +1,31 @@
+#!/bin/bash
+
+exit_status=0
+
+NXF_CMD=${NXF_CMD:-nextflow}
+NXF_FILES=${*:-'*.nf'}
+
+for pipeline in $NXF_FILES ; do
+
+    echo "> Running test: $pipeline"
+
+    # run the pipeline
+    $NXF_CMD -q run "$pipeline" > .out
+
+    # verify output (if ground truth exists)
+    outfile="$(basename "$pipeline" .nf).out"
+
+    if [[ -f "$outfile" ]] ; then
+        sort "$outfile" > a.out
+        sort .out > b.out
+        diff a.out b.out
+        status=$? ; [ $status -eq 0 ] || exit_status=$status
+    else
+        echo "> $outfile not found, skipping"
+    fi
+
+done
+
+rm -rf .nextflow* work .out a.out b.out
+
+[ $exit_status -eq 0 ] || false