From d13a967ef348576556544695d3a24a0858034573 Mon Sep 17 00:00:00 2001
From: Carol Scott <ces@sanger.ac.uk>
Date: Tue, 16 Jan 2024 15:27:48 +0000
Subject: [PATCH] Fix test

---
 Changes                                    |  1 -
 lib/npg_pipeline/function/seq_alignment.pm | 15 ++++++++++++---
 2 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/Changes b/Changes
index 60be640c..0cbed8c5 100644
--- a/Changes
+++ b/Changes
@@ -59,7 +59,6 @@ release 64.0.1
 release 64.0.0
  - add bwa_mem2 flag to options.pm to allow override of default bwa analyses at pipeline invocation
  - update seq_alignment to recognise the bwa_mem2 flag and also default to bwa_mem2 for NovaSeqX platform
->>>>>>> upstream/devel
 
 release 63.3.0
  - force no_target_alignment for haplotag libraries
diff --git a/lib/npg_pipeline/function/seq_alignment.pm b/lib/npg_pipeline/function/seq_alignment.pm
index 47f34ef4..adf4a7b5 100644
--- a/lib/npg_pipeline/function/seq_alignment.pm
+++ b/lib/npg_pipeline/function/seq_alignment.pm
@@ -489,7 +489,7 @@ sub _alignment_command { ## no critic (Subroutines::ProhibitExcessComplexity)
   else {
     push @{$p4_ops->{prune}}, 'foptgt.*samtools_stats_F0.*00_bait.*-';  # confirm hyphen
     if($p4_param_vals->{markdup_method} and ($p4_param_vals->{markdup_method} eq q[samtools] or $p4_param_vals->{markdup_method} eq q[picard])) {
-      push @{$p4_ops->{splice}}, 'ssfqc_tee_ssfqc:straight_through1:-foptgt_000_fixmate:', 'foptgt_000_markdup', 'foptgt_seqchksum_file:-scs_cmp_seqchksum:outputchk'; # the fixmate node only works for mardkup_method samtools (pending p4 node id uniqueness bug fix)
+      push @{$p4_ops->{splice}}, 'ssfqc_tee_ssfqc:straight_through1:-foptgt_000_fixmate:', 'foptgt_000_markdup', 'foptgt_seqchksum_file:-scs_cmp_seqchksum:outputchk'; # the fixmate node only works for markup_method samtools (pending p4 node id uniqueness bug fix)
     }
     else {
       push @{$p4_ops->{splice}}, 'ssfqc_tee_ssfqc:straight_through1:-foptgt_000_bamsort_coord:', 'foptgt_000_bammarkduplicates', 'foptgt_seqchksum_file:-scs_cmp_seqchksum:outputchk';
@@ -498,9 +498,18 @@ sub _alignment_command { ## no critic (Subroutines::ProhibitExcessComplexity)
 
   my $p4_local_assignments = {};
   if($do_gbs_plex){
-     if(my $gbb=npg_pipeline::cache::reference->instance->get_gbs_plex_bed_file($dp, $self->repository)) {
+
+     my $gbb;
+     try {
+        $gbb=npg_pipeline::cache::reference->instance->get_gbs_plex_bed_file($dp, $self->repository);
+     }
+     catch {
+        $self->info(qq[No reference defined so no primer clipping - $rpt_list]);
+     };
+
+     if (defined $gbb) {
         $p4_param_vals->{primer_clip_bed} = $gbb;
-        $self->info(qq[No markdup with gbs primer panel : $gbb]);
+        $self->info(qq[No markdup and primer clipping with gbs primer panel : $gbb]);
      } else {
         $p4_param_vals->{primer_clip_method} = q[no_clip];
      }