Commit adad218b authored by Boom's avatar Boom
Browse files

Test tool without localization.

parent e034874e
......@@ -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"
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment