Added a cleanup step for bcbio config and param files

docs/SOP_alignment_variant_annotation.md

@@ -215,4 +215,14 @@ cd /home/u035/u035/shared/analysis/reads/${project_id}
 rm `ls | grep -v -f retain_for_rerun.txt`
 ```
 
-10. Update the batch status spreadsheet. Move to [SOP prioritization](SOP_prioritization.md).
+10. Move the bcbio related parameter and config files into the results directory, leaving the family and PED files for the prioritization step.
+
+```
+cd $OUTPUT_DIR/${short_project_id}_${version}
+mkdir -p config
+mv $CONFIG_DIR/${short_project_id}_${version}* config/
+mkdir -p params
+mv $PARAMS_DIR/${short_project_id}_${version}* params/
+```
+
+11. Update the batch status spreadsheet. Move to [SOP prioritization](SOP_prioritization.md).