From adad218bbd6f501b0194107adf81cc9588ba91ba Mon Sep 17 00:00:00 2001
From: JasperBoom <jboom@infernum.nl>
Date: Mon, 14 Jun 2021 15:02:41 +0200
Subject: [PATCH] Test tool without localization.
---
bam2fastx.wdl | 21 +++------------------
1 file changed, 3 insertions(+), 18 deletions(-)
diff --git a/bam2fastx.wdl b/bam2fastx.wdl
index 4e5ed3e..3cdb29f 100644
--- a/bam2fastx.wdl
+++ b/bam2fastx.wdl
@@ -103,31 +103,16 @@ task Bam2Fastq {
String dockerImage = "quay.io/biocontainers/bam2fastx:1.3.1--hf05d43a_1"
}
- command <<<
+ command {
set -e
mkdir -p "$(dirname ~{outputPrefix})"
-
- # Localise the bam and pbi files so they are next to each other in the
- # current folder.
- bamFiles=""
- for bamFile in ~{sep=" " bam}
- do
- ln -s ${bamFile} ./
- bamFiles=${bamFiles}" ./$(basename ${bamFile})"
- done
-
- for indexFile in ~{sep=" " bamIndex}
- do
- ln -s ${indexFile} ./
- done
-
bam2fastq \
--output ~{outputPrefix} \
-c ~{compressionLevel} \
~{true="--split-barcodes" false="" splitByBarcode} \
~{"--seqid-prefix " + seqIdPrefix} \
- ${bamFiles}
- >>>
+ ~{bam}
+ }
output {
File fastqFile = outputPrefix + ".fastq.gz"
--
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