Commit 734c4037 authored by Boom's avatar Boom
Browse files

Try another approach.

parent adee85e2
......@@ -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"
......
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