Changeset 5773


Ignore:
Timestamp:
Dec 3, 2019, 1:40:58 PM (3 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:
1 edited

Legend:

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

    r5772 r5773  
    122122    script.cmd("cd ${TMPDIR}");
    123123    script.cmd("cp ${ScriptDir}/mut_stats.py .");
     124    script.cmd("mkdir results");
     125    script.cmd("mkdir tmp");
    124126    script.newLine();
    125127   
     
    128130    statCmd += " ${WD}/progress";
    129131    statCmd += " ${WD}/mut_stats.log";
    130     statCmd += " > mut_stats.vcf";
     132    statCmd += " > tmp/mut_stats.vcf";
    131133    script.cmd(statCmd);
    132134    script.progress(95, "Sorting and indexing...");
    133     script.cmd(bedtools_path+" sort -header -i mut_stats.vcf | bgzip -c > mut_stats.vcf.gz");
    134     script.cmd("tabix mut_stats.vcf.gz");
     135    script.cmd(bedtools_path+" sort -header -i tmp/mut_stats.vcf | bgzip -c > results/mut_stats.vcf.gz");
     136    script.cmd("tabix results/mut_stats.vcf.gz");
     137    script.cmd("cp results/* ${WD}");
    135138   
    136139    script.progress(99, "Cleaning up temporary folders");
     
    215218     
    216219      return "Parsed " + stat.numVcf + " VCF files for " + stat.numPatients + " patients." +
    217         " Found "+Reggie.formatCount(stat.numVariants) + " variants.";
     220        " Found "+Reggie.formatCount(stat.numVariants) + " variants." +
     221        " Result files can be found at: " + session.getHost().getWorkFolder(jobName);
    218222    }
    219223  }
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