From 0df52e802caa2e7f3793ec37f6378d8929bb6411 Mon Sep 17 00:00:00 2001
From: JasperBoom <jboom@infernum.nl>
Date: Tue, 1 Dec 2020 12:21:37 +0100
Subject: [PATCH] Remove naming.
---
lima.wdl | 20 ++++++++++----------
1 file changed, 10 insertions(+), 10 deletions(-)
diff --git a/lima.wdl b/lima.wdl
index 90cd698..2455aaa 100644
--- a/lima.wdl
+++ b/lima.wdl
@@ -83,26 +83,26 @@ task Lima {
~{true="--peek-guess" false="" peekGuess} \
--log-level ~{logLevel} \
--num-threads ~{threads} \
- ~{"--log-file " + outputPrefix + ".fl.stderr.log"} \
+ ~{"--log-file " + outputPrefix + ".lima.stderr.log"} \
~{inputBamFile} \
~{barcodeFile} \
- ~{outputPrefix + ".fl.bam"}
+ ~{outputPrefix + ".bam"}
dirName="$(dirname ~{outputPrefix})"
- find "$(cd ${dirName}; pwd)" -name "*.fl.*.bam" > bamFiles.txt
- find "$(cd ${dirName}; pwd)" -name "*.fl.*.bam.pbi" > bamIndexes.txt
- find "$(cd ${dirName}; pwd)" -name "*.fl.*.subreadset.xml" > subreadsets.txt
+ find "$(cd ${dirName}; pwd)" -name "*.bam" > bamFiles.txt
+ find "$(cd ${dirName}; pwd)" -name "*.bam.pbi" > bamIndexes.txt
+ find "$(cd ${dirName}; pwd)" -name "*.subreadset.xml" > subreadsets.txt
>>>
output {
Array[File] limaBam = read_lines("bamFiles.txt")
Array[File] limaBamIndex = read_lines("bamIndexes.txt")
Array[File] limaXml = read_lines("subreadsets.txt")
- File limaStderr = outputPrefix + ".fl.stderr.log"
- File limaJson = outputPrefix + ".fl.json"
- File limaCounts = outputPrefix + ".fl.lima.counts"
- File limaReport = outputPrefix + ".fl.lima.report"
- File limaSummary = outputPrefix + ".fl.lima.summary"
+ File limaStderr = outputPrefix + ".lima.stderr.log"
+ File limaJson = outputPrefix + ".json"
+ File limaCounts = outputPrefix + ".lima.counts"
+ File limaReport = outputPrefix + ".lima.report"
+ File limaSummary = outputPrefix + ".lima.summary"
}
runtime {
--
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