Update tests and output file names.

workflow/scripts/call_peaks_macs.py

@@ -126,7 +126,7 @@ def call_peaks_macs(experiment, xcor, control, prefix, genome_size, chrom_sizes)
     # Remove coordinates outside chromosome sizes
 
     int_narrowpeak_fn = '%s_peaks.narrowPeak' % (prefix)
-    narrowpeak_fn = '%s_peaks.narrowPeak' % (prefix)
+    narrowpeak_fn = '%s.narrowPeak' % (prefix)
     clipped_narrowpeak_fn = 'clipped-%s' % (narrowpeak_fn)
 
 

workflow/scripts/map_reads.py

@@ -104,7 +104,7 @@ def generate_sa(fastq, reference):
 def align_se(fastq, sai, reference, fastq_basename):
     '''Use BWA to align SE data.'''
 
-    bam_filename = '%s.srt.bam' % (fastq_basename)
+    bam_filename = '%s.bam' % (fastq_basename)
 
     steps = [
         "bwa samse %s %s %s"
@@ -125,7 +125,7 @@ def align_pe(fastq, sai, reference, fastq_basename):
 
     sam_filename = "%s.sam" % (fastq_basename)
     badcigar_filename = "%s.badReads" % (fastq_basename)
-    bam_filename = '%s.srt.bam' % (fastq_basename)
+    bam_filename = '%s.bam' % (fastq_basename)
 
     # Remove read pairs with bad CIGAR strings and sort by position
     steps = [

workflow/scripts/trim_reads.py

@@ -76,15 +76,15 @@ def rename_reads(fastq, sample, paired):
 
     if paired:  # paired-end data
         # Set file names
-        renamed_fastq.append(cwd + '/' + sample + '_R1.fastq.gz')
-        renamed_fastq.append(cwd + '/' + sample + '_R2.fastq.gz')
+        renamed_fastq.append(cwd + '/' + sample + '_R1.fq.gz')
+        renamed_fastq.append(cwd + '/' + sample + '_R2.fq.gz')
 
         # Great symbolic links
         os.symlink(fastq[0], renamed_fastq[0])
         os.symlink(fastq[1], renamed_fastq[1])
     else:
         # Set file names
-        renamed_fastq.append(cwd + '/' + sample + '_R1.fastq.gz')
+        renamed_fastq.append(cwd + '/' + sample + '_R1.fq.gz')
 
         # Great symbolic links
         os.symlink(fastq[0], renamed_fastq[0])

workflow/tests/test_convert_reads.py

@@ -9,8 +9,8 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
 
 @pytest.mark.singleend
 def test_convert_reads_singleend():
-    assert os.path.exists(os.path.join(test_output_path, 'ENCFF646LXU.tagAlign.gz'))
-    assert os.path.exists(os.path.join(test_output_path, 'ENCFF646LXU.bedse.gz'))
+    assert os.path.exists(os.path.join(test_output_path, 'ENCLB831RUI.tagAlign.gz'))
+    assert os.path.exists(os.path.join(test_output_path, 'ENCLB831RUI.bedse.gz'))
 
 
 @pytest.mark.pairedend

workflow/tests/test_trim_reads.py

@@ -13,9 +13,9 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
 @pytest.mark.singleend
 def test_trim_reads_singleend():
     raw_fastq = test_data_path + 'ENCFF833BLU.fastq.gz'
-    trimmed_fastq = test_output_path + 'ENCLB144FDT_trimmed.fq.gz'
+    trimmed_fastq = test_output_path + 'ENCLB144FDT_R1_trimmed.fq.gz'
     trimmed_fastq_report = test_output_path + \
-                            'ENCLB144FDT.fastq.gz_trimming_report.txt'
+                            'ENCLB144FDT_R1_trimmed.fq.gz_trimming_report.txt'
     assert os.path.getsize(raw_fastq) != os.path.getsize(trimmed_fastq)
     assert os.path.getsize(trimmed_fastq) == 2512853101
     assert 'Trimming mode: single-end' in open(trimmed_fastq_report).readlines()[4]
@@ -24,9 +24,9 @@ def test_trim_reads_singleend():
 @pytest.mark.pairedend
 def test_trim_reads_pairedend():
     raw_fastq = test_data_path + 'ENCFF582IOZ.fastq.gz'
-    trimmed_fastq = test_output_path + 'ENCFF582IOZ_val_2.fq.gz'
+    trimmed_fastq = test_output_path + 'ENCLB637LZP_R2_trimmed.fq.gz'
     trimmed_fastq_report = test_output_path + \
-                            'ENCLB637LZP.fastq.gz_trimming_report.txt'
+                            'ENCLB637LZP_R2_trimmed.fq.gz_trimming_report.txt'
     assert os.path.getsize(raw_fastq) != os.path.getsize(trimmed_fastq)
     assert os.path.getsize(trimmed_fastq) == 2229312710
     assert 'Trimming mode: paired-end' in open(trimmed_fastq_report).readlines()[4]

workflow/tests/test_xcor.py

@@ -10,8 +10,8 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
 
 @pytest.mark.singleend
 def test_cross_singleend():
-    assert os.path.exists(os.path.join(test_output_path, 'ENCFF833BLU.cc.plot.pdf'))
-    qc_file = os.path.join(test_output_path,"ENCFF833BLU.cc.qc")
+    assert os.path.exists(os.path.join(test_output_path, 'ENCLB144FDT.cc.plot.pdf'))
+    qc_file = os.path.join(test_output_path,"ENCLB144FDT.cc.qc")
     df_xcor = pd.read_csv(qc_file, sep="\t", header=None)
     assert df_xcor[2].iloc[0] == '190,200,210'
     assert df_xcor[8].iloc[0] == 1.025906