From 235fb43f046b285a3b5d8ca702b2cc8ad64dcf36 Mon Sep 17 00:00:00 2001
From: JasperBoom <jboom@infernum.nl>
Date: Tue, 15 Jun 2021 11:18:37 +0200
Subject: [PATCH] Revert changes to WDL file.
---
bam2fastx.wdl | 29 +++++++++++++++++------------
1 file changed, 17 insertions(+), 12 deletions(-)
diff --git a/bam2fastx.wdl b/bam2fastx.wdl
index 110441e..0bdccca 100644
--- a/bam2fastx.wdl
+++ b/bam2fastx.wdl
@@ -35,7 +35,7 @@ task Bam2Fasta {
String dockerImage = "quay.io/biocontainers/bam2fastx:1.3.1--hf05d43a_1"
}
- command <<<
+ command {
set -e
mkdir -p "$(dirname ~{outputPrefix})"
@@ -44,13 +44,13 @@ task Bam2Fasta {
bamFiles=""
for bamFile in ~{sep=" " bam}
do
- ln -s ${bamFile} ./
- bamFiles=${bamFiles}" ./$(basename ${bamFile})"
+ ln $bamFile .
+ bamFiles=$bamFiles" $(basename $bamFile)"
done
- for indexFile in ~{sep=" " bamIndex}
+ for index in ~{sep=" " bamIndex}
do
- ln -s ${indexFile} ./
+ ln $index .
done
bam2fasta \
@@ -58,8 +58,8 @@ task Bam2Fasta {
-c ~{compressionLevel} \
~{true="--split-barcodes" false="" splitByBarcode} \
~{"--seqid-prefix " + seqIdPrefix} \
- ${bamFiles}
- >>>
+ $bamFiles
+ }
output {
File fastaFile = outputPrefix + ".fasta.gz"
@@ -103,7 +103,7 @@ task Bam2Fastq {
String dockerImage = "quay.io/biocontainers/bam2fastx:1.3.1--hf05d43a_1"
}
- command <<<
+ command {
set -e
mkdir -p "$(dirname ~{outputPrefix})"
@@ -112,8 +112,13 @@ task Bam2Fastq {
bamFiles=""
for bamFile in ~{sep=" " bam}
do
- fullPathBam=$(readlink -f ${bamFile})
- bamFiles=${bamFiles}" ${fullPathBam}"
+ ln $bamFile .
+ bamFiles=$bamFiles" $(basename $bamFile)"
+ done
+
+ for index in ~{sep=" " bamIndex}
+ do
+ ln $index .
done
bam2fastq \
@@ -121,8 +126,8 @@ task Bam2Fastq {
-c ~{compressionLevel} \
~{true="--split-barcodes" false="" splitByBarcode} \
~{"--seqid-prefix " + seqIdPrefix} \
- ${bamFiles}
- >>>
+ $bamFiles
+ }
output {
File fastqFile = outputPrefix + ".fastq.gz"
--
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