| 6661 |
01 Apr 22 |
nicklas |
#!/bin/bash |
| 6661 |
01 Apr 22 |
nicklas |
2 |
|
| 6661 |
01 Apr 22 |
nicklas |
3 |
RUN_ARCHIVE=`find ${ALL_RUN_ARCHIVES} -maxdepth 2 -name ${DATA_FOLDER} -type d -print -quit 2> /dev/null || true` |
| 6661 |
01 Apr 22 |
nicklas |
4 |
if [ -z "$RUN_ARCHIVE" ]; then |
| 6661 |
01 Apr 22 |
nicklas |
5 |
echo "Can't find data folder ${DATA_FOLDER} in [${ALL_RUN_ARCHIVES}]" 1>&2 |
| 6661 |
01 Apr 22 |
nicklas |
6 |
exit 1 |
| 6661 |
01 Apr 22 |
nicklas |
7 |
fi |
| 6661 |
01 Apr 22 |
nicklas |
8 |
|
| 6678 |
19 Apr 22 |
nicklas |
9 |
${JAVA} \ |
| 6678 |
19 Apr 22 |
nicklas |
10 |
-Dpicard.useLegacyParser=false ${JavaOptions} \ |
| 6678 |
19 Apr 22 |
nicklas |
11 |
-jar ${PICARD} CheckIlluminaDirectory \ |
| 6678 |
19 Apr 22 |
nicklas |
12 |
-BASECALLS_DIR ${RUN_ARCHIVE}/Data/Intensities/BaseCalls \ |
| 6678 |
19 Apr 22 |
nicklas |
13 |
-READ_STRUCTURE ${READSTRING} \ |
| 6678 |
19 Apr 22 |
nicklas |
14 |
-DATA_TYPES BaseCalls \ |
| 6678 |
19 Apr 22 |
nicklas |
15 |
-LANES ${LANE} \ |
| 6678 |
19 Apr 22 |
nicklas |
16 |
-QUIET true |