From 8c8cc282377b4787e87680874f43bf37f4cac7ff Mon Sep 17 00:00:00 2001
From: JasperBoom <jboom@infernum.nl>
Date: Fri, 20 Mar 2020 16:42:09 +0100
Subject: [PATCH] Update lima to correctly collect bam files.
---
lima.wdl | 15 ++++++++-------
1 file changed, 8 insertions(+), 7 deletions(-)
diff --git a/lima.wdl b/lima.wdl
index 52f1697..125b12c 100644
--- a/lima.wdl
+++ b/lima.wdl
@@ -85,17 +85,18 @@ task Lima {
~{"--log-file " + outputPrefix + ".fl.stderr.log"} \
~{inputBamFile} \
~{barcodeFile} \
- ~{outputPrefix + ".fl.bam"}
+ ~{basename(outputPrefix) + ".fl.bam"}
}
output {
- File outputFLfile = outputPrefix + "*.bam"
- File outputFLindexFile = outputPrefix + "*.bam.pbi"
+ Array[File] outputFLfile = glob("~{basename(outputPrefix)}*.bam")
+ Array[File] outputFLindexFile = glob("~{basename(outputPrefix)}*.bam.pbi")
+ Array[File] outputFLxmlFile = glob("~{basename(outputPrefix)}*.subreadset.xml")
File outputSTDERRfile = outputPrefix + ".fl.stderr.log"
- File outputJSONfile = outputPrefix + ".fl.json"
- File outputCountsFile = outputPrefix + ".fl.lima.counts"
- File outputReportFile = outputPrefix + ".fl.lima.report"
- File outputSummaryFile = outputPrefix + ".fl.lima.summary"
+ File outputJSONfile = "~{basename(outputPrefix)}.fl.json"
+ File outputCountsFile = "~{basename(outputPrefix)}.fl.lima.counts"
+ File outputReportFile = "~{basename(outputPrefix)}.fl.lima.report"
+ File outputSummaryFile = "~{basename(outputPrefix)}.fl.lima.summary"
}
runtime {
--
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