From 7ba4c125163a377e0ce1bd2a0a29e98d17f3b978 Mon Sep 17 00:00:00 2001
From: JasperBoom <jboom@infernum.nl>
Date: Thu, 30 Jan 2020 13:47:07 +0100
Subject: [PATCH] Replace moving with hardlinking.
---
centrifuge.wdl | 12 ++++++++----
1 file changed, 8 insertions(+), 4 deletions(-)
diff --git a/centrifuge.wdl b/centrifuge.wdl
index 3f01d0e..909de67 100644
--- a/centrifuge.wdl
+++ b/centrifuge.wdl
@@ -115,9 +115,11 @@ task Classify {
command <<<
set -e
mkdir -p "$(dirname ~{outputPrefix})"
- indexPath=~{sub(indexFiles[0], "\.[0-9]\.cf", "")}
indexBasename="$(basename ~{sub(indexFiles[0], "\.[0-9]\.cf", "")})"
- mv ${indexPath}* $PWD/
+ for file in ~{sep=" " indexFiles}
+ do
+ ln ${file} $PWD/"$(basename ${file})"
+ done
centrifuge \
~{inputFormatOptions[inputFormat]} \
~{true="--phred64" false="--phred33" phred64} \
@@ -190,9 +192,11 @@ task Inspect {
command <<<
set -e
mkdir -p "$(dirname ~{outputPrefix})"
- indexPath=~{sub(indexFiles[0], "\.[0-9]\.cf", "")}
indexBasename="$(basename ~{sub(indexFiles[0], "\.[0-9]\.cf", "")})"
- mv ${indexPath}* $PWD/
+ for file in ~{sep=" " indexFiles}
+ do
+ ln ${file} $PWD/"$(basename ${file})"
+ done
centrifuge-inspect \
~{outputOptions[printOption]} \
~{"--across " + across} \
--
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