From 0696ab0603cf11fb4ec98dc3202207c668a9e511 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Tue, 19 Jun 2018 16:08:09 +0200
Subject: [PATCH] fix flatten
---
gatk.wdl | 14 ++++++++++----
1 file changed, 10 insertions(+), 4 deletions(-)
diff --git a/gatk.wdl b/gatk.wdl
index 9dbdfdd..66ff1a2 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -56,16 +56,22 @@ task BaseRecalibrator {
File inputBamIndex
String recalibrationReportPath
Array[File]+ sequenceGroupInterval
- Array[File?]? knownIndelsSitesVCFs
- Array[File?]? knownIndelsSitesIndices
+ Array[File]? knownIndelsSitesVCFs
+ Array[File]? knownIndelsSitesIndices
File? dbsnpVCF
File? dbsnpVCFindex
File refDict
File refFasta
File refFastaIndex
- Array[File]+ knownIndelsSitesVCFsArg = select_all(flatten([knownIndelsSitesVCFs, [dbsnpVCF]]))
- Array[File]+ knownIndelsSitesIndicesArg = select_all(flatten([knownIndelsSitesIndices, [dbsnpVCFindex]]))
+ Array[File]+ knownIndelsSitesVCFsArg = flatten([
+ select_first([knownIndelsSitesVCFs, []]),
+ select_all([dbsnpVCF])
+ ])
+ Array[File]+ knownIndelsSitesIndicesArg = flatten([
+ select_first([knownIndelsSitesIndices, []]),
+ select_all([dbsnpVCFindex])
+ ])
Float? memory
Float? memoryMultiplier
--
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