Commit 235fb43f authored by Boom's avatar Boom
Browse files

Revert changes to WDL file.

parent 734c4037
......@@ -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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