Changeset 5809


Ignore:
Timestamp:
Jan 13, 2020, 1:15:03 PM (2 years ago)
Author:
Nicklas Nordborg
Message:

References #1215: Include mutation signature analysis in the variant calling pipeline

Use the wrapper script to start the mutation signature R script.

File:
1 edited

Legend:

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

    r5795 r5809  
    352352      script.cmd("cp ${ScriptDir}/g5_dist.toml .");
    353353      script.cmd("cp ${ScriptDir}/mutation_signature.R .");
     354      script.cmd("cp ${ScriptDir}/Rscript.sh .");
    354355      script.cmd("mkdir bam");
    355356      script.cmd("mkdir mosdepth");
     
    479480        script.cmd("NUMFILTERED=`grep -c -v '^#' resultsfilter/variants-filtered.vcf || true`");
    480481        script.cmd("if [ $NUMFILTERED -gt 0 ]; then");
    481         String mutSignCmd = "./mutation_signature.R";
     482        String mutSignCmd = "./Rscript.sh ./mutation_signature.R";
    482483        mutSignCmd += " " + libName;
    483484        mutSignCmd += " resultsfilter/variants-filtered.vcf";
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