From 7c512fbd8fd7fac223ca580463e3f77e4bf9911e Mon Sep 17 00:00:00 2001
From: ffinfo <pjrvanthof@gmail.com>
Date: Wed, 12 Sep 2018 12:21:46 +0200
Subject: [PATCH] Change names
---
picard.wdl | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/picard.wdl b/picard.wdl
index 6de0a61..6fcf6b6 100644
--- a/picard.wdl
+++ b/picard.wdl
@@ -42,7 +42,7 @@ task BedToIntervalList {
task CollectMultipleMetrics {
input {
String? preCommand
- IndexedBamFile bam
+ IndexedBamFile bamFile
Reference reference
String basename
@@ -72,7 +72,7 @@ task CollectMultipleMetrics {
~{preCommand}
~{toolCommand} \
CollectMultipleMetrics \
- I=~{bam.file} \
+ I=~{bamFile.file} \
R=~{reference.fasta} \
O=~{basename} \
PROGRAM=null \
@@ -116,7 +116,7 @@ task CollectMultipleMetrics {
task CollectRnaSeqMetrics {
input {
String? preCommand
- IndexedBamFile bam
+ IndexedBamFile bamFile
File refRefflat
String basename
String strandSpecificity = "NONE"
@@ -137,7 +137,7 @@ task CollectRnaSeqMetrics {
~{preCommand}
~{toolCommand} \
CollectRnaSeqMetrics \
- I=~{bam.file} \
+ I=~{bamFile.file} \
O=~{basename}.RNA_Metrics \
CHART_OUTPUT=~{basename}.RNA_Metrics.pdf \
STRAND_SPECIFICITY=~{strandSpecificity} \
@@ -157,7 +157,7 @@ task CollectRnaSeqMetrics {
task CollectTargetedPcrMetrics {
input {
String? preCommand
- IndexedBamFile bam
+ IndexedBamFile bamFile
Reference reference
File ampliconIntervals
Array[File]+ targetIntervals
@@ -179,7 +179,7 @@ task CollectTargetedPcrMetrics {
~{preCommand}
~{toolCommand} \
CollectTargetedPcrMetrics \
- I=~{bam.file} \
+ I=~{bamFile.file} \
R=~{reference.fasta} \
AMPLICON_INTERVALS=~{ampliconIntervals} \
TARGET_INTERVALS=~{sep=" TARGET_INTERVALS=" targetIntervals} \
--
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