diff --git a/docs/SOP_archiving.md b/docs/SOP_archiving.md index 7cab069e62f00bbc578d681a4aa4891763311204..5c17c13aaa15c38b08d300da3ff1684858e44c9d 100644 --- a/docs/SOP_archiving.md +++ b/docs/SOP_archiving.md @@ -44,9 +44,7 @@ cd /home/u035/project/trio_whole_exome/analysis/logs ``` qsub -v \ - PROJECT_ID=$project_id,\ - VERSION=$version,\ - CONFIG_SH=/home/u035/project/scripts/trio_whole_exome_config.sh \ + PROJECT_ID=$project_id,VERSION=$version,CONFIG_SH=/home/u035/project/scripts/trio_whole_exome_config.sh \ -N trio_whole_exome_cram_compression.$project_id -J 1-${X} \ /home/u035/project/scripts/submit_trio_wes_cram_compression.sh ``` @@ -55,9 +53,7 @@ qsub -v \ ``` qsub -v \ - PROJECT_ID=$project_id,\ - VERSION=$version,\ - CONFIG_SH=/home/u035/project/scripts/trio_whole_exome_config.sh \ + PROJECT_ID=$project_id,VERSION=$version,CONFIG_SH=/home/u035/project/scripts/trio_whole_exome_config.sh \ -N trio_whole_exome_checksums.$project_id -J 1-${X} \ /home/u035/project/scripts/submit_trio_wes_checksums.sh cd ../output @@ -69,10 +65,7 @@ wc -l *$project_id*/md5sum.txt ``` priority_dirs=ddmmyyyy #:ddmmyyyy qsub -v \ - PROJECT_ID=$project_id,\ - VERSION=$version,\ - PRIORITY_DIRS=$priority_dirs,\ - CONFIG_SH=/home/u035/project/scripts/trio_whole_exome_config.sh \ + PROJECT_ID=$project_id,VERSION=$version,PRIORITY_DIRS=$priority_dirs,CONFIG_SH=/home/u035/project/scripts/trio_whole_exome_config.sh \ -N trio_whole_exome_priority_and_qc_checksums.$project_id \ /home/u035/project/scripts/submit_trio_wes_priority_and_qc_checksums.sh ``` @@ -81,10 +74,7 @@ qsub -v \ ``` qsub -v \ - PROJECT_ID=$project_id,\ - VERSION=$version,\ - PRIORITY_DIRS=$priority_dirs, \ - CONFIG_SH=/home/u035/project/scripts/trio_whole_exome_config.sh \ + PROJECT_ID=$project_id,VERSION=$version,PRIORITY_DIRS=$priority_dirs,CONFIG_SH=/home/u035/project/scripts/trio_whole_exome_config.sh \ -N trio_whole_exome_archive_project.$project_id \ /home/u035/project/scripts/submit_trio_wes_archive_project.sh grep -c FAIL trio_whole_exome_archive_project.$project_id*