Another test fix for keeping temps.

ukhsa-collaboration · Jun 24, 2016 · 98c8c64 · 98c8c64
1 parent 4ea6e20
commit 98c8c64
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/test/submit_jobs.py b/test/submit_jobs.py
@@ -73,7 +73,7 @@ def main():
 
 module load anaconda samtools/1.3 bwa/0.7.13 jdk picard-tools gatk bowtie2
     
-PYTHONPATH=.:$PYTHONPATH scripts/phenix.py run_snp_pipeline -r1 %(R1)s -r2 %(R2)s -r %(REF)s -c %(CONFIG)s --sample-name %(sample_name)s -o %(outdir)s
+PYTHONPATH=.:$PYTHONPATH scripts/phenix.py run_snp_pipeline --keep-temp -r1 %(R1)s -r2 %(R2)s -r %(REF)s -c %(CONFIG)s --sample-name %(sample_name)s -o %(outdir)s
     
 """ % params