From 06a48fb115f1a446a2b855cfa96d3b59bedf06bf Mon Sep 17 00:00:00 2001
From: ameyner2 <alison.meynert@ed.ac.uk>
Date: Wed, 21 Jul 2021 11:34:27 +0100
Subject: [PATCH] Moved output cleanup to main pipeline doc
---
docs/SOP_alignment_variant_annotation.md | 12 ++++++++++--
1 file changed, 10 insertions(+), 2 deletions(-)
diff --git a/docs/SOP_alignment_variant_annotation.md b/docs/SOP_alignment_variant_annotation.md
index 5cb7159..fbfa224 100644
--- a/docs/SOP_alignment_variant_annotation.md
+++ b/docs/SOP_alignment_variant_annotation.md
@@ -252,7 +252,15 @@ perl /home/u035/project/scripts/trio_whole_exome_parse_peddy_ped_csv.pl \
grep -v False$ qc/${version}_$project_id.ped_check.txt
```
-7. Clear the work directory and move the log files to the complete sub-directory.
+7. Clean up the output directory.
+
+```
+cd /home/u035/project/trio_whole_exome/
+mkdir ${version}_${project_id}
+mv *${version}_${project_id}* ${version}_${project_id}/
+```
+
+8. Clear the work directory and move the log files to the complete sub-directory.
```
cd /scratch/u035/project/trio_whole_exome/work
@@ -261,7 +269,7 @@ cd /home/u035/project/trio_whole_exome/logs
mv trio_whole_exome_bcbio.$project_id* complete/
```
-8. Copy the MultiQC report to the IGMM-VariantAnalysis area on the IGMM datastore.
+9. Copy the MultiQC report to the IGMM-VariantAnalysis area on the IGMM datastore.
```
ssh eddie3.ecdf.ed.ac.uk
--
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