all: chmod import_runqc import_read_counts copy_Exome_Diagnostik_diagnostic queue_Exome_Diagnostik_diagnostic queue_trios

chmod:
	chmod -R 775 Unaligned

import_runqc:
	php /mnt/storage2/megSAP/pipeline/src/NGS/runqc_parser.php -name "#01489" -run_dir Unaligned/../ -force

import_read_counts:
	php /mnt/storage2/megSAP/pipeline/src/NGS/import_sample_read_counts.php -stats Unaligned/Stats/Stats.json -db NGSD_TEST 

copy_Exome_Diagnostik_diagnostic:
	mv Unaligned/Exome_Diagnostik/Sample_DX203663_02/ /mnt/storage2/projects/diagnostic/Exome_Diagnostik/
	mv Unaligned/Exome_Diagnostik/Sample_DX203664_03/ /mnt/storage2/projects/diagnostic/Exome_Diagnostik/
	mv Unaligned/Exome_Diagnostik/Sample_DX203665_04/ /mnt/storage2/projects/diagnostic/Exome_Diagnostik/

queue_Exome_Diagnostik_diagnostic:
	php /mnt/storage2/megSAP/pipeline/src/NGS/db_queue_analysis.php -type 'single sample' -samples DX203663_02
	php /mnt/storage2/megSAP/pipeline/src/NGS/db_queue_analysis.php -type 'single sample' -samples DX203664_03
	php /mnt/storage2/megSAP/pipeline/src/NGS/db_queue_analysis.php -type 'single sample' -samples DX203665_04

queue_trios:
	php /mnt/storage2/megSAP/pipeline/src/NGS/db_queue_analysis.php -type 'trio' -samples DX203663_02 DX203665_04 DX203664_03 -info child father mother
