From 6eaf21442d9352266f0ac3e108cf1dc084c1c9f4 Mon Sep 17 00:00:00 2001
From: Redmar van den Berg <RedmarvandenBerg@lumc.nl>
Date: Wed, 7 Oct 2020 14:07:39 +0200
Subject: [PATCH] Ensure that the index and bamfiles are in the same folder
---
bam2fastx.wdl | 15 ++++++++++++++-
1 file changed, 14 insertions(+), 1 deletion(-)
diff --git a/bam2fastx.wdl b/bam2fastx.wdl
index 42240cd..1843475 100644
--- a/bam2fastx.wdl
+++ b/bam2fastx.wdl
@@ -91,12 +91,25 @@ task Bam2Fastq {
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 $bamfile .
+ bamfiles=$bamfiles" $(basename $bamfile)"
+ done
+
+ for bamindex in ~{sep=" " bamIndex}; do
+ ln $bamindex .
+ done
+
bam2fastq \
--output ~{outputPrefix} \
-c ~{compressionLevel} \
~{true="--split-barcodes" false="" splitByBarcode} \
~{"--seqid-prefix " + seqIdPrefix} \
- ~{sep=" " bam}
+ $bamfiles
}
output {
--
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