From f468bd568b5d9fcbd66872934837a4f88a4f2f0b Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Fri, 19 Feb 2021 16:43:57 +0100
Subject: [PATCH] add index to htseq

---
 htseq.wdl | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/htseq.wdl b/htseq.wdl
index dfa3fcf..ef4ae0a 100644
--- a/htseq.wdl
+++ b/htseq.wdl
@@ -23,6 +23,7 @@ version 1.0
 task HTSeqCount {
     input {
         Array[File]+ inputBams
+        Array[File]+ inputBamIndexes
         File gtfFile
         String outputTable = "output.tsv"
         String order = "pos"
@@ -34,7 +35,7 @@ task HTSeqCount {
 
         Int nprocesses = 1
         String memory = "8G"
-        Int timeMinutes = 10 + ceil(size(inputBams, "G") * 60)
+        Int timeMinutes = 1440 #10 + ceil(size(inputBams, "G") * 60) FIXME
         String dockerImage = "quay.io/biocontainers/htseq:0.12.4--py37hb3f55d8_0"
     }
 
-- 
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