fix: add count input to the demo WDL. (#25)

stjude-biohackathon · Sep 6, 2024 · a886a62 · a886a62
1 parent 829261e
commit a886a62
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Showing 2 changed files with 4 additions and 2 deletions.
diff --git a/crankshaft/demo.json b/crankshaft/demo.json
@@ -1,3 +1,4 @@
 {
-    "url": "https://www.encodeproject.org/files/ENCFF863PGO/@@download/ENCFF863PGO.bam"
+    "url": "https://www.encodeproject.org/files/ENCFF863PGO/@@download/ENCFF863PGO.bam",
+    "count": 100000
 }
diff --git a/crankshaft/demo.wdl b/crankshaft/demo.wdl
@@ -5,10 +5,11 @@ version 1.2
 task samtools_flagstat {
     input {
         String url
+        Int count = 100000
     }
 
     command <<<
-        samtools flagstat <(wget -O - -q '~{url}' | samtools view -h | head -n 100000)
+        samtools flagstat <(wget -O - -q '~{url}' | samtools view -h | head -n ~{count})
     >>>
 
     requirements {