From c331202b5ab6272289f7b84896d73679534bd6c0 Mon Sep 17 00:00:00 2001
From: not populated not populated <ameynert@sdf-cs1.eidf.epcc.ed.ac.uk>
Date: Mon, 4 Oct 2021 13:21:11 +0100
Subject: [PATCH] Added a cleanup step for bcbio config and param files

---
 docs/SOP_alignment_variant_annotation.md | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/docs/SOP_alignment_variant_annotation.md b/docs/SOP_alignment_variant_annotation.md
index 28973cc..2460170 100644
--- a/docs/SOP_alignment_variant_annotation.md
+++ b/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).
-- 
GitLab