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biowdl
tasks
Commits
a422e529
Commit
a422e529
authored
Jun 14, 2021
by
Boom
Browse files
Try a different approach.
parent
4f879f72
Changes
1
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bam2fastx.wdl
View file @
a422e529
...
...
@@ -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
cp
$bamFile ./
bamFiles=$bamFiles" ./$(basename $bamFile)"
ln -s
$
{
bamFile
}
./
bamFiles=$
{
bamFiles
}
" ./$(basename $
{
bamFile
}
)"
done
for index in ~{sep=" " bamIndex}
for index
File
in ~{sep=" " bamIndex}
do
cp
$index ./
ln -s
$
{
index
File}
./
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})"
...
...
@@ -112,13 +112,13 @@ task Bam2Fastq {
bamFiles=""
for bamFile in ~{sep=" " bam}
do
cp
$bamFile ./
bamFiles=$bamFiles" ./$(basename $bamFile)"
ln -s
$
{
bamFile
}
./
bamFiles=$
{
bamFiles
}
" ./$(basename $
{
bamFile
}
)"
done
for index in ~{sep=" " bamIndex}
for index
File
in ~{sep=" " bamIndex}
do
cp
$index ./
ln -s
$
{
index
File}
./
done
bam2fastq \
...
...
@@ -126,8 +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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