v1.1.0

scripts/pipeline.pl

@@ -101,7 +101,7 @@ =head1 Note:
 		die "[$task] Error! Can't make directory:\"$dir\"\n";
 	}
 }else {
-	my @f = <"$dir/mapping">;
+	my @f = <"$dir/mapping/*">;
 	if (@f) {
 			die "[$task] Directory $dir/mapping is not empty. Please specify another directory or a empty directory.\n";
 	}
@@ -327,7 +327,7 @@ =head1 Note:
 	#$busco_cmd .= "--tblastn   $software{tblastn}->{tblastn}     " if $software{tblastn}->{tblastn};    
 	#$busco_cmd .= "--augustus  $software{augustus}->{augustus}   " if $software{augustus}->{augustus};
 	#$busco_cmd .= "--hmmsearch $software{hmmsearch}->{hmmsearch} " if $software{hmmsearch}->{hmmsearch};
-	push @cmd, [0x0000, 0x0080, "Now running busco5.\n", $busco_cmd];
+	push @cmd, [0x0000, 0x0080, "Now running busco v5.\n", $busco_cmd];
 }
 
 ##running

scripts/run_busco5.pl

@@ -29,8 +29,8 @@
     --bbtools       path to bbtools stats.sh
 
 Note:
-    GAEP calls BUSCO in offline mode, so please provide an unpacked lineage 
-    dataset, which can be downloaded from https://busco-data.ezlab.org/v5/data/.
+    GAEP calls BUSCO in offline mode, so please provide an unpacked lineage dataset, 
+	which can be downloaded from https://busco-data.ezlab.org/v5/data/lineages/.
     If the paths of the dependencies are not specified in the command line, GAEP 
     will search for them in the environment.
 USAGE

scripts/summary.pl

@@ -22,6 +22,7 @@
 	0x0100 => "$prefix_out.base.qv",
 	0x0200 => "$dir/merqury_output/$prefix.qv",
 );
+$pipe{0x0080} = glob $pipe{0x0080};
 
 my %result = (
 	l1 => {},
@@ -129,7 +130,6 @@
 }
 
 if ($checkpoint & 0x0080 == 0x0080 && -e $pipe{0x0080}) {
-	$pipe{0x0080} = glob $pipe{0x0080};
 	my ($C, $D, $F) = (0,0,0);
 	open STAT, '<', $pipe{0x0080} or warn "[$task] Can't find $pipe{0x0080}.\n";
 	while (<STAT>) {