Fixed some bugs.

zy-optimistic · Jun 8, 2023 · c9db5b6 · c9db5b6
1 parent 19bdc32
commit c9db5b6
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Showing 4 changed files with 11 additions and 11 deletions.
diff --git a/scripts/pipeline.pl b/scripts/pipeline.pl
@@ -39,7 +39,7 @@ =head2 Global setting
 
 =head2 Busco setting
 
- -l           Busco lineage dataset, odb10(https://busco-data.ezlab.org/v5/data/) is supported, 
+ -l           Busco lineage dataset, odb10(https://busco-data.ezlab.org/v5/data/lineages/) is supported, 
               busco will not run without lineage dataset.
  -s           Species used for augustus training in busco.
 

diff --git a/scripts/run_hisat2.pl b/scripts/run_hisat2.pl
@@ -76,7 +76,7 @@
 my $out_file = "${prefix_out}_TRANS_mapping.bam";
 
 ##Creating a HISAT2 index
-my $index_cmd = "hisat2-build ";
+my $index_cmd = "$hisat2_build ";
 $index_cmd .= "-p $threads " if $threads;
 $index_cmd .= "$assembly $index";
 _system($index_cmd,$sys_run);
@@ -88,11 +88,11 @@
 	my $hisat2_paired_sort_bam = "$prefix_out.paired.sorted.bam";
 	#my $hisat2_paired_markdup = "$prefix_out.paired.sorted.mkdup.bam";
 	##run hisat2
-	my $hisat2_cmd = "hisat2 ";
+	my $hisat2_cmd = "$hisat2 ";
 	$hisat2_cmd .= "-p $threads " if $threads;
 	$hisat2_cmd .= "-x $index ";
 	for my $i ( 0..$#{ $flist{paired} } ) {
-		my $hisat2_cmd = "hisat2 ";
+		my $hisat2_cmd = "$hisat2 ";
 		$hisat2_cmd .= "-p $threads " if $threads;
 		$hisat2_cmd .= "-x $index ";
 		my $reads1 = $flist{paired}[$i][0];
@@ -117,7 +117,7 @@
 	$view_cmd .= "-bS $hisat2_paired_out > $hisat2_paired_bam";
 	_system($view_cmd, $sys_run);
 	##samtools sort
-	my $sort_cmd = "samtools sort ";
+	my $sort_cmd = "$samtools sort ";
 	$sort_cmd .= "-@ $threads " if $threads;
 	$sort_cmd .= "$hisat2_paired_bam -o $hisat2_paired_sort_bam";
 	_system ($sort_cmd,$sys_run);
@@ -134,7 +134,7 @@
 
 	##run hisat2
 	for my $i ( 0..$#{ $flist{single} } ){
-		my $hisat2_cmd = "hisat2 ";
+		my $hisat2_cmd = "$hisat2 ";
 		$hisat2_cmd .= "-p $threads " if $threads;
 		$hisat2_cmd .= "-x $index ";
 		my $reads1 = $flist{single}[0];
@@ -158,7 +158,7 @@
 	$view_cmd .= "-bS $hisat2_single_out > $hisat2_single_bam";
 	_system($view_cmd, $sys_run);
 	##samtools sort
-	my $sort_cmd = "samtools sort ";
+	my $sort_cmd = "$samtools sort ";
 	$sort_cmd .= "-@ $threads " if $threads;
 	$sort_cmd .= "$hisat2_single_bam -o $hisat2_single_sort_bam";
 	_system ($sort_cmd,$sys_run);

diff --git a/scripts/run_minimap2.pl b/scripts/run_minimap2.pl
@@ -111,7 +111,7 @@
 }
 
 ##sort
-my $sort_cmd = "samtools sort -O BAM ";
+my $sort_cmd = "$samtools sort -O BAM ";
 $sort_cmd .= "-@ $threads " if $threads;
 $temp = $sort_cmd;
 foreach (@sam_list){
@@ -122,7 +122,7 @@
 
 ##merge
 if (@file_list > 1){
-	my $merge_cmd = "samtools merge ";
+	my $merge_cmd = "$samtools merge ";
 	$merge_cmd .= "-@ $threads " if $threads;
 	$merge_cmd .= "-h $sam_list[0].sorted.bam $out_bam ";
 	$merge_cmd .= join (" ",map {"$_.sorted.bam"} @sam_list);

diff --git a/scripts/var_calling.pl b/scripts/var_calling.pl
@@ -66,7 +66,7 @@
 	_system($markdup_cmd, $mode);
 	$bam = $markdup;
 	#index
-	my $index_cmd = "samtools index ";
+	my $index_cmd = "$samtools index ";
 	$index_cmd .= "-@ $threads " if $threads;
 	$index_cmd .= "$bam";
 	_system($index_cmd, $mode);
@@ -93,7 +93,7 @@
 $semaphore->up($threads);
 
 ##merge all vcfs into one
-my $concat = "bcftools concat $prefix_out.*.flt.vcf > $var_result";
+my $concat = "$bcftools concat $prefix_out.*.flt.vcf > $var_result";
 _system($concat, $mode);