Changeset 5809

Timestamp:

Jan 13, 2020, 1:15:03 PM (4 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:

• extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/grid/VariantCallingJobCreator.java (modified) (2 diffs)

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

@@ -352 +352 @@
       script.cmd("cp ${ScriptDir}/g5_dist.toml .");
       script.cmd("cp ${ScriptDir}/mutation_signature.R .");
+      script.cmd("cp ${ScriptDir}/Rscript.sh .");
       script.cmd("mkdir bam");
       script.cmd("mkdir mosdepth");
@@ -479 +480 @@
         script.cmd("NUMFILTERED=`grep -c -v '^#' resultsfilter/variants-filtered.vcf || true`");
         script.cmd("if [ $NUMFILTERED -gt 0 ]; then");
-        String mutSignCmd = "./mutation_signature.R";
+        String mutSignCmd = "./Rscript.sh ./mutation_signature.R";
         mutSignCmd += " " + libName;
         mutSignCmd += " resultsfilter/variants-filtered.vcf";