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Update Bismark arguments
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primeseq/src/org/labkey/primeseq/pipeline/BismarkWrapper.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -137,7 +137,7 @@ public AlignmentOutput performAlignment(Readset rs, List<File> inputFastqs1, @Nu
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args.add("--samtools_path");
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args.add(new SamtoolsRunner(getPipelineCtx().getLogger()).getSamtoolsPath().getParentFile().getPath());
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args.add("--path_to_aligner");
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args.add("--path_to_bowtie2");
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args.add(getBowtie2Exe().getParentFile().getPath());
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if (getClientCommandArgs() != null)

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