Use common lib generate file function

BD2KGenomics · Sep 22, 2016 · 94f20c6 · 94f20c6
1 parent 4c319e6
commit 94f20c6
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/src/toil_scripts/gatk_germline/germline.py b/src/toil_scripts/gatk_germline/germline.py
@@ -56,7 +56,7 @@
 from toil_lib import require
 from toil_lib.programs import docker_call
 from toil_lib.urls import download_url_job
-from toil_scripts.rnaseq_cgl.rnaseq_cgl_pipeline import generate_file
+from toil_lib.files import generate_file
 from toil_lib.tools.aligners import run_bwakit
 from toil_lib.tools.indexing import run_samtools_faidx
 from toil_lib.tools.preprocessing import run_gatk_preprocessing, \
@@ -839,6 +839,7 @@ def main():
                            'preprocess',
                            'preprocess_only',
                            'run_vqsr',
+                           'run_hard_filter',
                            'joint_genotype',
                            'run_oncotator',
                            'cores',