Moved output cleanup to main pipeline doc

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