From 734c4037e642bf318b249f8835f2042c40ff328d Mon Sep 17 00:00:00 2001
From: JasperBoom <jboom@infernum.nl>
Date: Mon, 14 Jun 2021 15:49:53 +0200
Subject: [PATCH] Try another approach.
---
bam2fastx.wdl | 16 +++++++++++++---
1 file changed, 13 insertions(+), 3 deletions(-)
diff --git a/bam2fastx.wdl b/bam2fastx.wdl
index b09f7a0..110441e 100644
--- a/bam2fastx.wdl
+++ b/bam2fastx.wdl
@@ -103,16 +103,26 @@ task Bam2Fastq {
String dockerImage = "quay.io/biocontainers/bam2fastx:1.3.1--hf05d43a_1"
}
- command {
+ command <<<
set -e
mkdir -p "$(dirname ~{outputPrefix})"
+
+ # Localise the bam and pbi files so they are next to each other in the
+ # current folder.
+ bamFiles=""
+ for bamFile in ~{sep=" " bam}
+ do
+ fullPathBam=$(readlink -f ${bamFile})
+ bamFiles=${bamFiles}" ${fullPathBam}"
+ done
+
bam2fastq \
--output ~{outputPrefix} \
-c ~{compressionLevel} \
~{true="--split-barcodes" false="" splitByBarcode} \
~{"--seqid-prefix " + seqIdPrefix} \
- ~{sep=" " bam}
- }
+ ${bamFiles}
+ >>>
output {
File fastqFile = outputPrefix + ".fastq.gz"
--
GitLab