Merge pull request #231 from dozy/tophat_hs_aln

use bwa aln for human split with tophat target alignment
wtsi-npg · Jun 26, 2017 · 108635c · 108635c
2 parents c4f2568 + 6628a9c
commit 108635c
Show file tree

Hide file tree

Showing 2 changed files with 6 additions and 2 deletions.
diff --git a/Changes b/Changes
@@ -1,6 +1,9 @@
 LIST OF CHANGES
 ---------------
 
+release 51.10.2
+ - use bwa aln for human split with tophat target alignment
+
 release 51.10.1
  - Modified qc run function list, removed copy_interop and switched archive_to_irods to samplesheet
 

diff --git a/lib/npg_pipeline/archive/file/generation/seq_alignment.pm b/lib/npg_pipeline/archive/file/generation/seq_alignment.pm
@@ -313,8 +313,9 @@ sub _lsf_alignment_command { ## no critic (Subroutines::ProhibitExcessComplexity
     $p4_param_vals->{alignment_method} = q[tophat2];
     if($do_target_alignment) { $p4_param_vals->{alignment_reference_genome} = $self->_ref($l,q(bowtie2)); }
     if($nchs) {
-      $p4_param_vals->{hs_alignment_reference_genome} = $self->_default_human_split_ref(q{bowtie2}, $self->repository);
-      $p4_param_vals->{alignment_hs_method} = q[tophat2];
+      # this human split alignment method is currently the same as the default, but this may change
+      $p4_param_vals->{hs_alignment_reference_genome} = $self->_default_human_split_ref(q{bwa0_6}, $self->repository);
+      $p4_param_vals->{alignment_hs_method} = $hs_bwa;
     }
   }
   else {