diff runAssembly_cDNA_wrapper.pl @ 3:bf1f8bc4abe6 default tip

minor updates for v2.6

--- a/runAssembly_cDNA_wrapper.pl	Thu Jul 14 22:14:07 2011 -0400
+++ b/runAssembly_cDNA_wrapper.pl	Wed Dec 21 19:42:53 2011 -0800
@@ -22,6 +22,7 @@
 my $scaffolds_fasta=shift @ARGV;
 my $scaffolds_qual=shift @ARGV;
 my $scaffolds_agp=shift @ARGV;
+my $contig_scaffolds_agp=shift @ARGV;
 my $tag_pair_align=shift @ARGV;
 my $trim_status=shift @ARGV;
 my $isotigs_ace=shift @ARGV;
@@ -35,9 +36,8 @@
 my @cmd=removeUnusedOptions(@ARGV);
 
 # RUN COMMAND
-# NOTE: FIRST ARG EXPECTED TO BE EXECUTABLE
 my $stderr;
-eval { $stderr=`@cmd 2>&1`; };
+eval { $stderr=`runAssembly @cmd 2>&1`; };
 if ( $@ ) {
     print STDERR "Newbler ERROR: $stderr\n";
     `cat $outdir/assembly/454NewblerProgress.txt 1>&2`;
@@ -59,6 +59,7 @@
 get_outfile("$outdir/454Scaffolds.fna", $scaffolds_fasta);
 get_outfile("$outdir/454Scaffolds.qual", $scaffolds_qual);
 get_outfile("$outdir/454Scaffolds.txt", $scaffolds_agp);
+get_outfile("$outdir/454ContigScaffolds.txt", $contig_scaffolds_agp);
 get_outfile("$outdir/454TagPairAlign.txt", $tag_pair_align);
 get_outfile("$outdir/454TrimStatus.txt", $trim_status);
 get_outfile("$outdir/454Isotigs.ace", $isotigs_ace);