Merge branch '15_Annotation_diff_bind' into 23-rename_output

workflow/conf/biohpc.config

@@ -14,19 +14,19 @@ process {
   }
   withName: alignReads{
     module = ['python/3.6.1-2-anaconda', 'bwa/intel/0.7.12', 'samtools/1.6']
-    cpus = 32
+    queue = '128GB,256GB,256GBv1'
   }
   withName: filterReads{
     module = ['python/3.6.1-2-anaconda', 'samtools/1.6', 'sambamba/0.6.6', 'bedtools/2.26.0']
-    cpus = 32
+    queue = '128GB,256GB,256GBv1'
   }
   withName: experimentQC {
     module = ['python/3.6.1-2-anaconda', 'deeptools/2.5.0.1']
-    cpus = 32
+    queue = '128GB,256GB,256GBv1'
   }
   withName: convertReads {
     module = ['python/3.6.1-2-anaconda',  'samtools/1.6', 'bedtools/2.26.0']
-    cpus = 32
+    queue = '128GB,256GB,256GBv1'
   }
   withName: crossReads {
     module = ['python/3.6.1-2-anaconda', 'phantompeakqualtools/1.2']
@@ -42,7 +42,7 @@ process {
   }
   withName: callPeaksMACS {
     module = ['python/3.6.1-2-anaconda', 'macs/2.1.0-20151222', 'phantompeakqualtools/1.2', 'UCSC_userApps/v317', 'bedtools/2.26.0']
-    cpus = 32
+    queue = '128GB,256GB,256GBv1'
   }
   withName: consensusPeaks {
     module = ['python/3.6.1-2-anaconda', 'bedtools/2.26.0']

workflow/tests/test_annotate_peaks.py

@@ -21,8 +21,8 @@ def test_annotate_peaks_singleend():
 
 @pytest.mark.pairedend
 def test_annotate_peaks_pairedend():
-    assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA..chipseeker_pie.pdf'))
-    assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA..chipseeker_upsetplot.pdf'))
-    annotation_file = test_output_path + 'ENCSR729LGA..chipseeker_annotation.csv'
+    assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA.chipseeker_pie.pdf'))
+    assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA.chipseeker_upsetplot.pdf'))
+    annotation_file = test_output_path + 'ENCSR729LGA.chipseeker_annotation.csv'
     assert os.path.exists(annotation_file)
-    assert utils.count_lines(annotation_file) == 25391
+    assert utils.count_lines(annotation_file) == 25614

workflow/tests/test_overlap_peaks.py

@@ -44,4 +44,4 @@ def test_overlap_peaks_singleend():
 def test_overlap_peaks_pairedend():
     assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA.rejected.narrowPeak'))
     peak_file = test_output_path + 'ENCSR729LGA.replicated.narrowPeak'
-    assert utils.count_lines(peak_file) == 25655
+    assert utils.count_lines(peak_file) == 25878