Change to using django templates for generating condor fastq scripts

[htsworkflow.git] / htsworkflow / templates / qseq.condor

diff --git a/htsworkflow/templates/qseq.condor b/htsworkflow/templates/qseq.condor
new file mode 100644 (file)
index 0000000..fcdac83
--- /dev/null
+++ b/htsworkflow/templates/qseq.condor
@@ -0,0 +1,11 @@
+Universe=vanilla
+executable={{ exe }}
+error={{ logdir }}/fastq.$(process).out
+output={{ logdir }}/fastq.$(process).out
+log={{ logdir }}/fastq.log
+{% if env %}environment={{ env }}{% endif %}
+
+{% for arg in args %}
+arguments="{{ arg.pyscript }} -o {{ arg.target }} {% if arg.flowcell %}-f {{ arg.flowcell }}{% endif %} {% if arg.istar %}-i{% endif %} {% for s in arg.sources %}{{ s }} {% endfor %}"
+queue
+{% endfor %}