Output cleanup moved to main pipeline SOP

docs/SOP_archiving.md

@@ -70,15 +70,7 @@ qsub -v \
   /home/u035/project/scripts/submit_trio_wes_priority_and_qc_checksums.sh
 ```
 
-5. Clean up the output directory.
-
-```
-cd /home/u035/project/trio_whole_exome/
-mkdir ${version}_${project_id}
-mv *${version}_${project_id}* ${version}_${project_id}/
-```
-
-6. Archive the output to /archive/u035/trio_whole_exome, excluding the BAM files. Confirm md5 checksums on the archived files. There should be no lines ending in ‘FAIL’. If there are any, investigate which file(s) and manually copy these, then re-check the md5 of the archived copy.
+5. Archive the output to /archive/u035/trio_whole_exome, excluding the BAM files. Confirm md5 checksums on the archived files. There should be no lines ending in ‘FAIL’. If there are any, investigate which file(s) and manually copy these, then re-check the md5 of the archived copy.
 
 ```
 qsub -v \
@@ -88,14 +80,14 @@ qsub -v \
 grep -c FAIL trio_whole_exome_archive_project.$project_id*
 ```
 
-7. Clean up the logs directory.
+6. Clean up the logs directory.
 
 ```
 cd /home/u035/project/trio_whole_exome/logs 
 mv *.project_id.* complete/
 ```
 
-8. Confirmation of copy to tape. EPCC runs a cron job on Monday mornings at 8am to check the DMF file state for all files in /archive/u035/trio_whole_exome. This produces a text report at /archive/u035/confirmation using the format yyyy-mm-dd. 
+7. Confirmation of copy to tape. EPCC runs a cron job on Monday mornings at 8am to check the DMF file state for all files in /archive/u035/trio_whole_exome. This produces a text report at /archive/u035/confirmation using the format yyyy-mm-dd. 
 
 Check for ‘DUL’ entries for files in the confirmation report. The grep command below excludes directories, which are generally marked as ‘REG’, blank lines, and total file size lines. If not all entries are DUL, check the non-DUL ones for error states as below. The expectation is that some files may be in the process of migration; in which case, check again in the following week’s report.