From a9a09f6483877fb9ebb9150e4d461c0a67b16662 Mon Sep 17 00:00:00 2001
From: Korneel Duyvesteyn <korneel.duyvesteyn@gmail.com>
Date: Tue, 29 May 2018 11:59:26 +0200
Subject: [PATCH] DEV-161: Remove amber baf from links

---
 lib/HMF/Pipeline/Amber.pm | 5 +----
 requirements.txt          | 2 +-
 2 files changed, 2 insertions(+), 5 deletions(-)

diff --git a/lib/HMF/Pipeline/Amber.pm b/lib/HMF/Pipeline/Amber.pm
index ee88e8c..fdf1538 100644
--- 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
index 87f04da..a526a9c 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1 +1 @@
-Cython==0.25.2
+# This file is needed for the build process.