2prev

Author: mikessh

src/main/groovy/com/milaboratory/migec/Assemble.groovy

@@ -34,7 +34,7 @@ cli.h("usage")
 cli.q(args: 1, argName: "read quality (phred)",
         "barcode region quality threshold. Default: $Util.DEFAULT_UMI_QUAL_THRESHOLD")
 cli._(longOpt: "mask", args: 1, argName: "X:Y, X=0/1, Y=0/1",
-        "Mask for read(s) in pair that should be assembled. Default: \"$DEFAULT_ASSEMBLE_MASK\".")
+        "Mask for read(s) in pair that should be assembled. Default: $DEFAULT_ASSEMBLE_MASK.")
 cli.p(args: 1,
         "number of threads to use. Default: all available processors")
 cli.c("compressed output")

src/main/groovy/com/milaboratory/migec/AssembleBatch.groovy

@@ -23,7 +23,8 @@ def DEFAULT_ASSEMBLE_MASK = "1:1", DEFAULT_PARENT_CHILD_RATIO = "0.1",
 def cli = new CliBuilder(usage: 'AssembleBatch [options] checkout_dir/ histogram_dir/ output_dir/')
 cli.h("usage")
 cli.p(args: 1, 'number of threads to use')
-cli._(longOpt: 'default-mask', args: 1, "Mask, default for all samples, see --sample-metadata")
+cli._(longOpt: 'default-mask', args: 1, "Mask, default for all samples, see --sample-metadata. " +
+        "Default: $DEFAULT_ASSEMBLE_MASK.")
 cli._(longOpt: 'sample-metadata', args: 1, argName: 'file name',
         "A tab-delimited file indicating which samples to process and containing three columns:\n" +
                 "sample_name (tab) file_type (tab) mask\n" +