Changeset 5773

Timestamp:

Dec 3, 2019, 1:40:58 PM (4 years ago)

Author:

Nicklas Nordborg

Message:

References #1208: Implement wizard for building database of variant frequencies in SCAN-B samples

Results files are now saved to the job folder which should preserve them after the job has finished.

File:

• extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/grid/VariantStatisticsJobCreator.java (modified) (3 diffs)

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/grid/VariantStatisticsJobCreator.java

@@ -122 +122 @@
     script.cmd("cd ${TMPDIR}");
     script.cmd("cp ${ScriptDir}/mut_stats.py .");
+    script.cmd("mkdir results");
+    script.cmd("mkdir tmp");
     script.newLine();
     
@@ -128 +130 @@
     statCmd += " ${WD}/progress";
     statCmd += " ${WD}/mut_stats.log";
-    statCmd += " > mut_stats.vcf";
+    statCmd += " > tmp/mut_stats.vcf";
     script.cmd(statCmd);
     script.progress(95, "Sorting and indexing...");
-    script.cmd(bedtools_path+" sort -header -i mut_stats.vcf | bgzip -c > mut_stats.vcf.gz");
-    script.cmd("tabix mut_stats.vcf.gz");
+    script.cmd(bedtools_path+" sort -header -i tmp/mut_stats.vcf | bgzip -c > results/mut_stats.vcf.gz");
+    script.cmd("tabix results/mut_stats.vcf.gz");
+    script.cmd("cp results/* ${WD}");
     
     script.progress(99, "Cleaning up temporary folders");
@@ -215 +218 @@
       
       return "Parsed " + stat.numVcf + " VCF files for " + stat.numPatients + " patients." + 
-        " Found "+Reggie.formatCount(stat.numVariants) + " variants.";
+        " Found "+Reggie.formatCount(stat.numVariants) + " variants." + 
+        " Result files can be found at: " + session.getHost().getWorkFolder(jobName);
     }
   }