Merge pull request #531 from mgcam/no-bcftools1

use default bcftools executable
wtsi-npg · Jun 20, 2018 · 7e082d1 · 7e082d1
2 parents f7aa39e + 2bf3bc6
commit 7e082d1
Show file tree

Hide file tree

Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/lib/npg_qc/autoqc/checks/genotype.pm b/lib/npg_qc/autoqc/checks/genotype.pm
@@ -29,7 +29,7 @@ Readonly::Scalar my $SAMTOOLS_NAME => q[samtools];
 Readonly::Scalar my $SAMTOOLS_EXTRACT_REGIONS_NAME => q[samtools];
 Readonly::Scalar my $SAMTOOLS_MERGE_NAME => q[samtools];
 Readonly::Scalar my $SAMTOOLS_MPILEUP_NAME => q[samtools];
-Readonly::Scalar my $BCFTOOLS_NAME => q[bcftools1];
+Readonly::Scalar my $BCFTOOLS_NAME => q[bcftools];
 Readonly::Scalar our $EXT => q[bam];
 Readonly::Scalar my $SEQUENOM_QC_PLEX => q[W30467];
 Readonly::Scalar my $DEFAULT_QC_PLEX => q[sequenom_fluidigm_combo];

diff --git a/lib/npg_qc/utils/bam_genotype.pm b/lib/npg_qc/utils/bam_genotype.pm
@@ -23,7 +23,7 @@ our $VERSION = '0';
 
 ##no critic
 Readonly::Scalar my $SAMTOOLS_NAME => 'samtools';
-Readonly::Scalar my $BCFTOOLS_NAME => 'bcftools1';
+Readonly::Scalar my $BCFTOOLS_NAME => 'bcftools';
 
 subtype '_bamgt_ReadableFile'
       => as Str

diff --git a/t/60-autoqc-checks-genotype.t b/t/60-autoqc-checks-genotype.t
@@ -15,7 +15,7 @@ my $dir = tempdir(CLEANUP => 1);
 my $st = join q[/], $dir, q[samtools];
 `touch $st`;
 `chmod +x $st`;
-my $bt = join q[/], $dir, q[bcftools1];
+my $bt = join q[/], $dir, q[bcftools];
 `touch $bt`;
 `chmod +x $bt`;
 local $ENV{PATH} = join q[:], $dir, $ENV{PATH};