Commit f2f7411a authored by Boom's avatar Boom
Browse files

Add directory creation to samtools fastq.

parent 235fb43f
......@@ -10,8 +10,7 @@ that users understand how the changes affect the new version.
version 5.0.0-dev
---------------------------
+ Change the way localization of the input bam files and index are handled
in the bam2fastx tasks.
+ Samtools: Add mkdir line to `Fastq` task.
+ Add new parameters from CCS version 6.0.0 and add two new outputs:
`ccs_report.txt` & `zmw_metrics.json.gz`.
+ Change CutAdapt memory to `5G`.
......
......@@ -122,6 +122,8 @@ task Fastq {
}
command {
set -e
mkdir -p "$(dirname ~{outputRead1})"
samtools fastq \
~{true="-1" false="-s" defined(outputRead2)} ~{outputRead1} \
~{"-2 " + outputRead2} \
......
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