DEV-161: Remove amber baf from links

hartwigmedical · May 29, 2018 · a9a09f6 · a9a09f6
1 parent 0c3ce1d
commit a9a09f6
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Showing 2 changed files with 2 additions and 5 deletions.
diff --git a/lib/HMF/Pipeline/Amber.pm b/lib/HMF/Pipeline/Amber.pm
@@ -39,16 +39,13 @@ sub run {
     push @amber_jobs, markDone($done_file, \@amber_jobs, $dirs, $opt);
     push @{$opt->{RUNNING_JOBS}->{'amber'}}, @amber_jobs;
 
-    my $baf_txt_path = "${sub_dir}/${tumor_sample}.amber.baf";
-    linkArtefact($baf_txt_path, 'somatic_amber_baf', $opt);
-
     return;
 }
 
 sub runAmber {
     my ($tumor_sample, $ref_bam_path, $tumor_bam_path, $running_jobs, $dirs, $opt) = @_;
 
-    say "\n### SCHEDULING AMBER ###";
+    say "\n### SCHEDULING AMBER MAIN ###";
     my $job_id = fromTemplate(
         "Amber",
         undef,

diff --git a/requirements.txt b/requirements.txt
@@ -1 +1 @@
-Cython==0.25.2
+# This file is needed for the build process.
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		Cython==0.25.2
		# This file is needed for the build process.